[gmx-users] Position restraints
Dear All! I have a doubt about the rightness of ligand/molecule integration in the topology file. I'm using an amber (tleap) or swissparam.ch to build a topology of the residue (modified trna). Is it neccessary to generate a position restrain file (genrestr program) for this residue or not? I've started both dynamics with/without posrestraints on my residue, however I'm really not sure that my results from both of them are different. But I want to do everything in right way, so what can you say about this? Thank you -- * Nemo me impune lacessit* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints
On 4/2/13 6:07 AM, alex rayevsky wrote: Dear All! I have a doubt about the rightness of ligand/molecule integration in the topology file. I'm using an amber (tleap) or swissparam.ch to build a topology of the residue (modified trna). Is it neccessary to generate a position restrain file (genrestr program) for this residue or not? I've started both dynamics with/without posrestraints on my residue, however I'm really not sure that my results from both of them are different. But I want to do everything in right way, so what can you say about this? Restraints during equilibration are used to prevent unnatural forces from the unequilibrated solvent and help prevent deformation of the structure. It's never a bad idea to restrain the whole solute. If I were reading a paper that described restraining the whole solute, except for one residue because it was special or difficult to deal with, I would immediately be suspicious. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Hi Dear Justin First of all, I request you that not to shout at me! I am so sorry to ask you questions about position restraints again! I know I have sent you such emails before, and you suggested me to read include file mechanism in web site. I did this and also read some emails in forum. But I think I have problems with include mechanism. Again I got into the trouble about position restraining: As you told me -DPOSRES will not trigger #ifdef POSRE or #ifdef DPOSRES. I have a system of POPC/ions/waters and a double chain protein inserted in POPC bilayer. I put restraints on P headgroups and protein. I added the define line to the mdp file as follow: define = -DPOSRES_LIPID -DPOSRES Then added the itp files to my top as follow: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif But when I run the grompp with -pp flag, I see that restraints on chain_B are not included! Then I changed the numbering in protein_chain_B_posre.itp to what they are in their original itp file, generated earlier by pdb2gmx. Do you agree that it is the problem which I encountered with? Now when I run grompp I see the restraints after each chains with the same numbering. Sincerely, Shima Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 12:02 AM Subject: Re: [gmx-users] position restraints On 3/25/13 3:25 PM, Shima Arasteh wrote: Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly. Say I have a system of arbitrary molecules that have 4 atoms each. Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule. Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive. Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error. What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified. So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file. If, for instance, P is atom number 8: [ position_restraints ] 8 1 0 0 1000 That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only. Hopefully that all makes sense and this experience has been educational as far as how these things work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
On 3/26/13 7:01 AM, Shima Arasteh wrote: Hi Dear Justin First of all, I request you that not to shout at me! I am so sorry to ask you questions about position restraints again! I haven't done any shouting, but statements like this seem to imply that I have. The point of this forum is post your questions, so if things still aren't clear, then you're welcome to post them. Hopefully I have never given anyone the impression of anger or castigation in my answers. Sometimes I am terse, but that's because I'm busy with my own work, and a short answer is preferable to a long one. I know I have sent you such emails before, and you suggested me to read include file mechanism in web site. I did this and also read some emails in forum. But I think I have problems with include mechanism. Again I got into the trouble about position restraining: As you told me -DPOSRES will not trigger #ifdef POSRE or #ifdef DPOSRES. I have a system of POPC/ions/waters and a double chain protein inserted in POPC bilayer. I put restraints on P headgroups and protein. I added the define line to the mdp file as follow: define= -DPOSRES_LIPID -DPOSRES Then added the itp files to my top as follow: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif #ifdef POSRE requires -DPOSRE, not -DPOSRES as you have above. I've now said that three times (and you said it above!), so please be mindful of the advice you've been given and take care in what you're doing. ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif But when I run the grompp with -pp flag, I see that restraints on chain_B are not included! I don't see how that's possible. Position restraints for both chains are under the control of the same #ifdef condition, as shown above. One cannot be restrained without the other. Then I changed the numbering in protein_chain_B_posre.itp to what they are in their original itp file, generated earlier by pdb2gmx. Do you agree that it is the problem which I encountered with? pdb2gmx should have provided you with suitable restraint .itp files when you produced the original topology, and will have written suitable #ifdef blocks to properly use them. Have you manipulated these files in some way? If you have, start over. Use the files that pdb2gmx gave you until you can convince yourself that you know how to use them correctly, then apply whatever custom restraints you feel are necessary. Learn to walk before you run. Now when I run grompp I see the restraints after each chains with the same numbering. I don't exactly know what this means. Are chains A and B identical? If they are, then this makes sense. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
No, You have not shouted at me, never! But sometimes I think that I deserve to be shouted !! I deeply appreciate your patience and attention. Thanks for your time and your replies. In my protein, chains A and B are identical. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 4:16 PM Subject: Re: [gmx-users] position restraints On 3/26/13 7:01 AM, Shima Arasteh wrote: Hi Dear Justin First of all, I request you that not to shout at me! I am so sorry to ask you questions about position restraints again! I haven't done any shouting, but statements like this seem to imply that I have. The point of this forum is post your questions, so if things still aren't clear, then you're welcome to post them. Hopefully I have never given anyone the impression of anger or castigation in my answers. Sometimes I am terse, but that's because I'm busy with my own work, and a short answer is preferable to a long one. I know I have sent you such emails before, and you suggested me to read include file mechanism in web site. I did this and also read some emails in forum. But I think I have problems with include mechanism. Again I got into the trouble about position restraining: As you told me -DPOSRES will not trigger #ifdef POSRE or #ifdef DPOSRES. I have a system of POPC/ions/waters and a double chain protein inserted in POPC bilayer. I put restraints on P headgroups and protein. I added the define line to the mdp file as follow: define = -DPOSRES_LIPID -DPOSRES Then added the itp files to my top as follow: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif #ifdef POSRE requires -DPOSRE, not -DPOSRES as you have above. I've now said that three times (and you said it above!), so please be mindful of the advice you've been given and take care in what you're doing. ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif But when I run the grompp with -pp flag, I see that restraints on chain_B are not included! I don't see how that's possible. Position restraints for both chains are under the control of the same #ifdef condition, as shown above. One cannot be restrained without the other. Then I changed the numbering in protein_chain_B_posre.itp to what they are in their original itp file, generated earlier by pdb2gmx. Do you agree that it is the problem which I encountered with? pdb2gmx should have provided you with suitable restraint .itp files when you produced the original topology, and will have written suitable #ifdef blocks to properly use them. Have you manipulated these files in some way? If you have, start over. Use the files that pdb2gmx gave you until you can convince yourself that you know how to use them correctly, then apply whatever custom restraints you feel are necessary. Learn to walk before you run. Now when I run grompp I see the restraints after each chains with the same numbering. I don't exactly know what this means. Are chains A and B identical? If they are, then this makes sense. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
On 3/26/13 8:39 AM, Shima Arasteh wrote: No, You have not shouted at me, never! But sometimes I think that I deserve to be shouted !! I deeply appreciate your patience and attention. Thanks for your time and your replies. In my protein, chains A and B are identical. If they are identical, then so too should be the position restraint files. In this case, it is still confusing in my mind (really, impossible) that one chain gets restrained and the other doesn't. How are you assessing whether or not the restraints are being applied? Can you quantitatively demonstrate that the restraints are not working? Applying restraints to a protein is a fairly rudimentary task, especially when handled by pdb2gmx topologies. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] position restraints
On Tue, Mar 26, 2013 at 1:01 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Have a look at processed topology file here please; I see that position restraints are brought after chain_A but not brought after chain_B. With these settings: ; Include chain topologies #ifdef POSRES #include topol_Protein_chain_A.itp #include protein_chain_A_posre.itp #endif #ifdef POSRES #include topol_Protein_chain_B.itp #include protein_chain_B_posre.itp #endif The above approach is incorrect. The inclusion of protein topologies is dependent upon using position restraints? That's certainly not right, especially if you ever want to run a simulation without restraints. The following is the correct approach: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif Also adding define = -DPOSRES_LIPID -DPOSRES , I get this processed.top: #grompp -f nvt.mdp -c minim.gro -p topol.top -n index.ndx -o nvt.tpr -pp THIS IS THE PROCESSED TOPOLOGY: ;File 'topol.top' was generated ;By user: shima (1000) ;On host: linux-cbyo.site ;At date: Wed Dec 12 12:17:51 2012 ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.5 ; ;Command line was: ;pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p ; ;Force field was read from current directory or a relative path - path added. ; ; Include forcefield parameters ; Conversion of CHARMM36 parameters to GROMACS format by Thomas Piggot, July 2010. ; Also added some parameters from later CHARMM27 versions, such as those for the PS headgroup. ; ; If you use these parameters please check out the forcefield.doc for papers to cite [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 ; ; Added new and changed old atomtypes and pairtypes (OSL, OSLP, HBL and CCL) - Thomas Pigot July 2010 ; [ atomtypes ] ;nameat.nummasschargeptypesigmaepsilon C612.011000.51A0.3563594872560.46024 CA612.01100-0.115A0.3550053212050.29288 CC612.011000.62A0.3563594872560.29288 CD612.011000.000A0.3563594872560.29288 ; partial charge def not found CE1612.011000.000A0.3723956641830.284512 ; partial charge def not found . . . . XNN1CN1AX9180.010.462 XNN2CN3BX9180.04.1842 XCN3CN3CX9180.00.41842 XNN2CN3CX9180.00.41842 XON4P3X90.01.25523 [ dihedraltypes ] ; ijklfuncq0cq NN2BCN4CN5HN220.058.576 NN2GCN4CN1HN220.06.6944 NN1CN2HN1HN120.050.208 CN1NN2GCN5GON120.0753.12 CN1TNN2BNN2UON120.0920.48 CN1NN2UCN3TON120.0753.12 CN2NN3GNN2GNN120.0334.72 CN2NN3ACN5NN120.0334.72 CN2NN3CN3NN120.0502.08 CN4NN2GNN3IHN320.0326.352 CN3CN3CCN8HN620.0125.52 HN2CN3CN3BNN220.0418.4 HN1HN1CN1ANN120.0-41.84 HN8CN3CN3CN820.0150.624 HR1NR1NR2CPH220.004.184 HR1NR2NR1CPH220.004.184 HR3CPH1NR1CPH120.004.184 HR3CPH1NR2CPH120.004.184 HR3NR1CPH1CPH120.004.184 HR3NR2CPH1CPH120.004.184 NR1CPH1CPH2CN7B20.005.0208 NR1CPH2CPH1CN7B20.005.0208 HN2XXNN220.08.368 HN1XXNN120.033.472 CN1XXON120.0753.12 CN1TXXON120.0753.12 CN1XXON1C20.0669.44 CN2XXNN120.0753.12 CN9XXCN3T20.0117.152 HN3BXXCN320.0125.52 HN3BXXCN3A20.0108.784 HN3BXXCN3B20.0108.784 ON1XXCN1A20.0334.72 HN3XXCN3C20.0443.504 HN6XXCN3C20.0443.504 ; Include chain topologies ; ;File 'topol_Protein_chain_A.itp' was generated ;By user: shima (1000) ;On host: linux-cbyo.site ;At date: Wed Dec 12 12:17:55 2012 ; ;This is a include topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.5 ; ;Command line was: ;pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p ; ;Force field was read from current directory
Re: Fw: [gmx-users] position restraints
1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 MG 1 MG MG 1 2 [ moleculetype ] ; molname nrexcl K 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 POT 1 K K 1 1 [ moleculetype ] ; molname nrexcl Ces 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CES 1 Ces Ces 1 1 [ moleculetype ] ; molname nrexcl Cal 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CAL 1 Cal Cal 1 2 [ moleculetype ] ; molname nrexcl CL 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CLA 1 CL CL 1 -1 [ moleculetype ] ; molname nrexcl ZN 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 ZN 1 ZN ZN 1 -2 [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 18706 NA 615 CL 617 Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 9:55 PM Subject: Re: Fw: [gmx-users] position restraints On Tue, Mar 26, 2013 at 1:01 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Have a look at processed topology file here please; I see that position restraints are brought after chain_A but not brought after chain_B. With these settings: ; Include chain topologies #ifdef POSRES #include topol_Protein_chain_A.itp #include protein_chain_A_posre.itp #endif #ifdef POSRES #include topol_Protein_chain_B.itp #include protein_chain_B_posre.itp #endif The above approach is incorrect. The inclusion of protein topologies is dependent upon using position restraints? That's certainly not right, especially if you ever want to run a simulation without restraints. The following is the correct approach: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif Also adding define = -DPOSRES_LIPID -DPOSRES , I get this processed.top: #grompp -f nvt.mdp -c minim.gro -p topol.top -n index.ndx -o nvt.tpr -pp THIS IS THE PROCESSED TOPOLOGY: ; File 'topol.top' was generated ; By user: shima (1000) ; On host: linux-cbyo.site ; At date: Wed Dec 12 12:17:51 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p ; ; Force field was read from current directory or a relative path - path added. ; ; Include forcefield parameters ; Conversion of CHARMM36 parameters to GROMACS format by Thomas Piggot, July 2010. ; Also added some parameters from later CHARMM27 versions, such as those for the PS headgroup. ; ; If you use these parameters please check out the forcefield.doc for papers to cite [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 ; ; Added new and changed old atomtypes and pairtypes (OSL, OSLP, HBL and CCL) - Thomas Pigot July 2010 ; [ atomtypes ] ;name at.num mass charge ptype sigma epsilon C 6 12.01100 0.51 A 0.356359487256 0.46024 CA 6 12.01100 -0.115 A 0.355005321205 0.29288 CC 6 12.01100 0.62 A 0.356359487256 0.29288 CD 6 12.01100 0.000 A 0.356359487256 0.29288 ; partial charge def not found CE1 6 12.01100 0.000 A 0.372395664183 0.284512 ; partial charge def not found . . . . X NN1 CN1A X 9 180.0 10.46 2 X NN2 CN3B X 9 180.0 4.184 2 X CN3 CN3C X 9 180.0 0.4184 2 X NN2 CN3C X 9 180.0 0.4184 2 X ON4 P3 X 9 0.0 1.2552 3 [ dihedraltypes ] ; i j k l func q0 cq NN2B CN4 CN5 HN2 2 0.0 58.576 NN2G CN4 CN1 HN2 2 0.0 6.6944 NN1 CN2 HN1 HN1 2 0.0 50.208 CN1 NN2G CN5G ON1 2 0.0 753.12 CN1T NN2B NN2U ON1 2 0.0 920.48 CN1 NN2U CN3T ON1 2 0.0 753.12 CN2 NN3G NN2G NN1 2 0.0 334.72 CN2 NN3A CN5 NN1 2 0.0 334.72 CN2 NN3 CN3 NN1 2 0.0 502.08 CN4 NN2G NN3I HN3 2 0.0 326.352 CN3 CN3C CN8 HN6 2 0.0 125.52 HN2 CN3 CN3B NN2 2 0.0 418.4 HN1 HN1 CN1A
Re: Fw: [gmx-users] position restraints
On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: The inclusion part was edited again in original top file. I dont know why I had written that! Sorry. But about last itp files, which you mentioned that they are created incorrectly, 1) I 'd like to know what itp file should be created? In my own, I just included the chain_B.itp file with the same numbering as the chain_A.itp file. I don't really know what that means. You should be using the files pdb2gmx gave you, at least until you understand how all of this works. You should not have to deal with anything related to restraining the protein. Hence why I've suggested that you start over. 2) One more thing, restraints for both chains are brought just one time in the processed.top file? I thought after each chain, the restraints which are included should be brought and written in processed.top file!!! They should. But what you showed makes no sense. Restraints can't correspond to atoms that don't exist and there should only ever be on [ position_restraints ] directive per [ moleculetype ]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] position restraints
Thanks for all your explanations. What I get as a conclusion is this: itp files are dependent to the numbering of aoms in molecule type directive and not any other things! Each posre.itp file created by genrestr should be in consistent with the molculetype numbering! Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, March 26, 2013 10:54 PM Subject: Re: Fw: [gmx-users] position restraints On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: The inclusion part was edited again in original top file. I dont know why I had written that! Sorry. But about last itp files, which you mentioned that they are created incorrectly, 1) I 'd like to know what itp file should be created? In my own, I just included the chain_B.itp file with the same numbering as the chain_A.itp file. I don't really know what that means. You should be using the files pdb2gmx gave you, at least until you understand how all of this works. You should not have to deal with anything related to restraining the protein. Hence why I've suggested that you start over. 2) One more thing, restraints for both chains are brought just one time in the processed.top file? I thought after each chain, the restraints which are included should be brought and written in processed.top file!!! They should. But what you showed makes no sense. Restraints can't correspond to atoms that don't exist and there should only ever be on [ position_restraints ] directive per [ moleculetype ]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] position restraints
On Tue, Mar 26, 2013 at 2:33 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Thanks for all your explanations. What I get as a conclusion is this: itp files are dependent to the numbering of aoms in molecule type directive and not any other things! Each posre.itp file created by genrestr should be in consistent with the molculetype numbering! Yes, exactly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position restraints
Hi, I want to use position restraints on P atom types of POPC, and on my protein inserted in POPC. The inserted protein has 2 chains. 1. I made index files for each chain and then restrained them by these commands: #make_ndx -f minim.gro -o protein_chain_A.ndx #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 -n protein_chain_A.ndx #make_ndx -f minim.gro -o protein_chain_B.ndx #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 -n protein_chain_B.ndx #make_ndx -f minim.gro -o lipid_posre.ndx #genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n lipid_posre.ndx 2. Then these lines added to top of the itp files: #ifdef POSRE #endif 3. Then restrained them as follow in top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRE_LIPID #include lipid_posre.itp #endif 4. Also added the define statement to mdp file : define = -DPOSRES_LIPID -DPOSRES But when I run the grompp and get the per-processed top, only the chain_A is included in position restraint! Would you please give me suggestions? They would be appreciated. Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
On 3/25/13 12:06 PM, Shima Arasteh wrote: Hi, I want to use position restraints on P atom types of POPC, and on my protein inserted in POPC. The inserted protein has 2 chains. 1. I made index files for each chain and then restrained them by these commands: #make_ndx -f minim.gro -o protein_chain_A.ndx #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 -n protein_chain_A.ndx #make_ndx -f minim.gro -o protein_chain_B.ndx #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 -n protein_chain_B.ndx #make_ndx -f minim.gro -o lipid_posre.ndx #genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n lipid_posre.ndx 2. Then these lines added to top of the itp files: #ifdef POSRE #endif 3. Then restrained them as follow in top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRE_LIPID #include lipid_posre.itp #endif 4. Also added the define statement to mdp file : define= -DPOSRES_LIPID -DPOSRES But when I run the grompp and get the per-processed top, only the chain_A is included in position restraint! Would you please give me suggestions? They would be appreciated. Again, POSRE and POSRES are different. -DPOSRES will not trigger the #ifdef POSRE block. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Believe me I add this line to mdp file as you wrote in KALP-15-DPPC. define = -DPOSRES_LIPID Also added these to top file. #ifdef POSRES_LIPID #include lipid_posre.itp #endif But I get again this error that the This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :(( Would you please help me? Thanks for help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 8:52 PM Subject: Re: [gmx-users] position restraints On 3/25/13 12:06 PM, Shima Arasteh wrote: Hi, I want to use position restraints on P atom types of POPC, and on my protein inserted in POPC. The inserted protein has 2 chains. 1. I made index files for each chain and then restrained them by these commands: #make_ndx -f minim.gro -o protein_chain_A.ndx #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 -n protein_chain_A.ndx #make_ndx -f minim.gro -o protein_chain_B.ndx #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 -n protein_chain_B.ndx #make_ndx -f minim.gro -o lipid_posre.ndx #genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n lipid_posre.ndx 2. Then these lines added to top of the itp files: #ifdef POSRE #endif 3. Then restrained them as follow in top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRE_LIPID #include lipid_posre.itp #endif 4. Also added the define statement to mdp file : define = -DPOSRES_LIPID -DPOSRES But when I run the grompp and get the per-processed top, only the chain_A is included in position restraint! Would you please give me suggestions? They would be appreciated. Again, POSRE and POSRES are different. -DPOSRES will not trigger the #ifdef POSRE block. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
On 3/25/13 1:40 PM, Shima Arasteh wrote: Believe me I add this line to mdp file as you wrote in KALP-15-DPPC. I believe what I see. If you're trying to re-type from memory what's in your topology and/or .mdp file, that's not productive. Please copy and paste to make efficient use of everyone's time. define= -DPOSRES_LIPID Also added these to top file. #ifdef POSRES_LIPID #include lipid_posre.itp #endif But I get again this error that the This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :(( Would you please help me? I've been trying, and it appears you're either giving inconsistent or incorrect information. Copy and paste directly from your .top file whatever sections are relevant. You also haven't said what is in lipid_posre.itp, which can be another source of problems. You just said you've created it with genrestr, but you didn't say what group you included. The numbering in the position restraint file is per [moleculetype], not the global atom numbering in the coordinate file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Yes sir! What I have in my top file is : ; Include forcefield parameters #include ./charmm36-modified.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 18706 NA 615 CL 617 I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 10:13 PM Subject: Re: [gmx-users] position restraints On 3/25/13 1:40 PM, Shima Arasteh wrote: Believe me I add this line to mdp file as you wrote in KALP-15-DPPC. I believe what I see. If you're trying to re-type from memory what's in your topology and/or .mdp file, that's not productive. Please copy and paste to make efficient use of everyone's time. define = -DPOSRES_LIPID Also added these to top file. #ifdef POSRES_LIPID #include lipid_posre.itp #endif But I get again this error that the This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :(( Would you please help me? I've been trying, and it appears you're either giving inconsistent or incorrect information. Copy and paste directly from your .top file whatever sections are relevant. You also haven't said what is in lipid_posre.itp, which can be another source of problems. You just said you've created it with genrestr, but you didn't say what group you included. The numbering in the position restraint file is per [moleculetype], not the global atom numbering in the coordinate file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
On 3/25/13 1:50 PM, Shima Arasteh wrote: Yes sir! What I have in my top file is : ; Include forcefield parameters #include ./charmm36-modified.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 POPC238 SOL 18706 NA 615 CL 617 I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know. In that case, lipid_posre.itp should have only one line. If you've made an index group of multiple P atoms across multiple molecules, that is the incorrect approach. Consult the manual, website, and numerous threads in the archive. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms? Thanks for your suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 10:22 PM Subject: Re: [gmx-users] position restraints On 3/25/13 1:50 PM, Shima Arasteh wrote: Yes sir! What I have in my top file is : ; Include forcefield parameters #include ./charmm36-modified.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 18706 NA 615 CL 617 I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know. In that case, lipid_posre.itp should have only one line. If you've made an index group of multiple P atoms across multiple molecules, that is the incorrect approach. Consult the manual, website, and numerous threads in the archive. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
On 3/25/13 2:47 PM, Shima Arasteh wrote: Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms? What you need to understand is how the position restraint mechanism works. If you know that, you can make .itp files by hand using a text editor if you like (which is actually what I do in the case of one-liners like lipid_posre.itp for what you're doing). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Yes, you are right. Because I have read the include mechanism in website many times, but I dont undrestand it in deep! :-( I may need to study more. Thanks Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 11:20 PM Subject: Re: [gmx-users] position restraints On 3/25/13 2:47 PM, Shima Arasteh wrote: Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms? What you need to understand is how the position restraint mechanism works. If you know that, you can make .itp files by hand using a text editor if you like (which is actually what I do in the case of one-liners like lipid_posre.itp for what you're doing). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
On 3/25/13 3:00 PM, Shima Arasteh wrote: Yes, you are right. Because I have read the include mechanism in website many times, but I dont undrestand it in deep! :-( I may need to study more. I would again suggest focusing more on the position restraints contents themselves. Your formulation for #including them is correct. The contents of lipid_posre.itp are not. There is substantial discussion on the topic of position restraints in the manual, as well as the help description of genrestr (especially the part that starts with WARNING), which I am willing to bet will solve your issues if you read it carefully. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 11:34 PM Subject: Re: [gmx-users] position restraints On 3/25/13 3:00 PM, Shima Arasteh wrote: Yes, you are right. Because I have read the include mechanism in website many times, but I dont undrestand it in deep! :-( I may need to study more. I would again suggest focusing more on the position restraints contents themselves. Your formulation for #including them is correct. The contents of lipid_posre.itp are not. There is substantial discussion on the topic of position restraints in the manual, as well as the help description of genrestr (especially the part that starts with WARNING), which I am willing to bet will solve your issues if you read it carefully. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
On 3/25/13 3:25 PM, Shima Arasteh wrote: Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly. Say I have a system of arbitrary molecules that have 4 atoms each. Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule. Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive. Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error. What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified. So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file. If, for instance, P is atom number 8: [ position_restraints ] 8 1 001000 That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only. Hopefully that all makes sense and this experience has been educational as far as how these things work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Ohhh...! :-) I could not get it on my own independently! Thanks for all your explanation! Many many thanks. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 12:02 AM Subject: Re: [gmx-users] position restraints On 3/25/13 3:25 PM, Shima Arasteh wrote: Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly. Say I have a system of arbitrary molecules that have 4 atoms each. Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule. Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive. Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error. What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified. So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file. If, for instance, P is atom number 8: [ position_restraints ] 8 1 0 0 1000 That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only. Hopefully that all makes sense and this experience has been educational as far as how these things work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the fatal error. This error states that I have inserted topology section position_restraints in a wrong place. I checked again the itp files included in my top file. They are matched correctly! Did I modified the settings incorrectly? What would be other potent problems? Please help me. Thanks for your help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, March 17, 2013 5:19 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/17/13 6:50 AM, Shima Arasteh wrote: Thanks for your replies. As you suggested, I did as follows: 1. made index groups of two chains of my protein 2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -n index-chain.ndx 3.Next, I included the itp files as follow in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef DPOSRE #include chainA_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef DPOSRE #include chainB_posre.itp #endif 4. I also added this line to my mdp file: define = -DPOSRE 5. In addition I added these at the top of itp files for bothe restrained chains: #ifdef DPOSRE #endif Now when I run the command : grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr I don't get any errors. But when I run the mdrun I don't see any position restraint terms in my log file. Would you please let me know your suggestions in this about? Did I do any steps by mistake? Yes, again there is a problem with the #ifdef statements. If you use: #ifdef DPOSRE ... #endif the corresponding define statement is -DDPOSRE. Think of the first D in the define statement as I am defining the following string to be true. Your .mdp file corresponds to the use of: #ifdef POSRE ... #endif -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
Thanks for all your replies. But I' d like to know what the meanings of S and D are? Why sometimes we should write DPOSRE, sometimes POSRE, and sometimes DPOSRES? Sincerely, Shima From: Shima Arasteh shima_arasteh2...@yahoo.com To: Justin Lemkul jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, March 18, 2013 10:35 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the fatal error. This error states that I have inserted topology section position_restraints in a wrong place. I checked again the itp files included in my top file. They are matched correctly! Did I modified the settings incorrectly? What would be other potent problems? Please help me. Thanks for your help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, March 17, 2013 5:19 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/17/13 6:50 AM, Shima Arasteh wrote: Thanks for your replies. As you suggested, I did as follows: 1. made index groups of two chains of my protein 2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -n index-chain.ndx 3.Next, I included the itp files as follow in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef DPOSRE #include chainA_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef DPOSRE #include chainB_posre.itp #endif 4. I also added this line to my mdp file: define = -DPOSRE 5. In addition I added these at the top of itp files for bothe restrained chains: #ifdef DPOSRE #endif Now when I run the command : grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr I don't get any errors. But when I run the mdrun I don't see any position restraint terms in my log file. Would you please let me know your suggestions in this about? Did I do any steps by mistake? Yes, again there is a problem with the #ifdef statements. If you use: #ifdef DPOSRE ... #endif the corresponding define statement is -DDPOSRE. Think of the first D in the define statement as I am defining the following string to be true. Your .mdp file corresponds to the use of: #ifdef POSRE ... #endif -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: Fwd: [gmx-users] position restraints
With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I don't know if this range of deviation with position restraints is sensible or not! I can't believe with such a force of 10 I still see deviations! I'd prefer to get less deviation. Would it be possible by using a greater fc ? Is it sensible? Thanks for your suggestions in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, March 16, 2013 12:24 AM Subject: Re: Fw: Fwd: [gmx-users] position restraints On 3/15/13 8:50 AM, Shima Arasteh wrote: Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? No, 0.2 nm is very high. With position restraints, offhand I would think around 0.05 nm or less would be indicative of proper restraints. This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Yes, using genrestr to create a suitable posre.itp file that includes only backbone atoms. -Justin Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/18/13 3:05 AM, Shima Arasteh wrote: To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the fatal error. This error states that I have inserted topology section position_restraints in a wrong place. I checked again the itp files included in my top file. They are matched correctly! Did I modified the settings incorrectly? Clearly. Fatal errors mean something is very wrong. In principle, what you showed before was correct. If that wasn't an actual topology snippet or you've done something else wrong, then I haven't seen what it is. -Justin What would be other potent problems? Please help me. Thanks for your help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, March 17, 2013 5:19 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/17/13 6:50 AM, Shima Arasteh wrote: Thanks for your replies. As you suggested, I did as follows: 1. made index groups of two chains of my protein 2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -n index-chain.ndx 3.Next, I included the itp files as follow in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef DPOSRE #include chainA_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef DPOSRE #include chainB_posre.itp #endif 4. I also added this line to my mdp file: define = -DPOSRE 5. In addition I added these at the top of itp files for bothe restrained chains: #ifdef DPOSRE #endif Now when I run the command : grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr I don't get any errors. But when I run the mdrun I don't see any position restraint terms in my log file. Would you please let me know your suggestions in this about? Did I do any steps by mistake? Yes, again there is a problem with the #ifdef statements. If you use: #ifdef DPOSRE ... #endif the corresponding define statement is -DDPOSRE. Think of the first D in the define statement as I am defining the following string to be true. Your .mdp file corresponds to the use of: #ifdef POSRE ... #endif -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/18/13 3:42 AM, Shima Arasteh wrote: Thanks for all your replies. But I' d like to know what the meanings of S and D are? Why sometimes we should write DPOSRE, sometimes POSRE, and sometimes DPOSRES? I already explained what the D prefix means. If this is unclear to you, please read about cpp macros. When processing a topology, grompp works just like cpp works on C source code. The choice between POSRE and POSRES is completely irrelevant except for your own usage and consistency in so doing. Gromacs defaults to using POSRES to indicate POSition REStraints. If you build some custom topology, you can use whatever you want. it doesn't matter at all, as long as you are consistent in invoking it. -Justin Sincerely, Shima From: Shima Arasteh shima_arasteh2...@yahoo.com To: Justin Lemkul jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, March 18, 2013 10:35 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the fatal error. This error states that I have inserted topology section position_restraints in a wrong place. I checked again the itp files included in my top file. They are matched correctly! Did I modified the settings incorrectly? What would be other potent problems? Please help me. Thanks for your help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, March 17, 2013 5:19 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/17/13 6:50 AM, Shima Arasteh wrote: Thanks for your replies. As you suggested, I did as follows: 1. made index groups of two chains of my protein 2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -n index-chain.ndx 3.Next, I included the itp files as follow in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef DPOSRE #include chainA_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef DPOSRE #include chainB_posre.itp #endif 4. I also added this line to my mdp file: define = -DPOSRE 5. In addition I added these at the top of itp files for bothe restrained chains: #ifdef DPOSRE #endif Now when I run the command : grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr I don't get any errors. But when I run the mdrun I don't see any position restraint terms in my log file. Would you please let me know your suggestions in this about? Did I do any steps by mistake? Yes, again there is a problem with the #ifdef statements. If you use: #ifdef DPOSRE ... #endif the corresponding define statement is -DDPOSRE. Think of the first D in the define statement as I am defining the following string to be true. Your .mdp file corresponds to the use of: #ifdef POSRE ... #endif -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: Fwd: [gmx-users] position restraints
On 3/18/13 6:02 AM, Shima Arasteh wrote: With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I don't know if this range of deviation with position restraints is sensible or not! I can't believe with such a force of 10 I still see deviations! I'd prefer to get less deviation. Would it be possible by using a greater fc ? Is it sensible? Were restraints correctly applied? Your last messages indicated fatal errors in trying to apply restraints - have you overcome those problems? Is there a position restraint energy term written to the .log and .edr files? Using such a huge force constant should not result in such RMSD values unless (1) they are not being applied or (2) whatever groups you have created for applying restraints do not cover all atoms that are being analyzed in the RMSD calculation, i.e. some are unrestrained and moving normally when you think they are being restrained. -Justin Thanks for your suggestions in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, March 16, 2013 12:24 AM Subject: Re: Fw: Fwd: [gmx-users] position restraints On 3/15/13 8:50 AM, Shima Arasteh wrote: Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? No, 0.2 nm is very high. With position restraints, offhand I would think around 0.05 nm or less would be indicative of proper restraints. This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Yes, using genrestr to create a suitable posre.itp file that includes only backbone atoms. -Justin Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On Mon, Mar 18, 2013 at 1:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 3:42 AM, Shima Arasteh wrote: Thanks for all your replies. But I' d like to know what the meanings of S and D are? Why sometimes we should write DPOSRE, sometimes POSRE, and sometimes DPOSRES? I already explained what the D prefix means. If this is unclear to you, please read about cpp macros. When processing a topology, grompp works just like cpp works on C source code. See also http://www.gromacs.org/Documentation/Include_File_Mechanism Mark The choice between POSRE and POSRES is completely irrelevant except for your own usage and consistency in so doing. Gromacs defaults to using POSRES to indicate POSition REStraints. If you build some custom topology, you can use whatever you want. it doesn't matter at all, as long as you are consistent in invoking it. -Justin Sincerely, Shima __**__ From: Shima Arasteh shima_arasteh2...@yahoo.com To: Justin Lemkul jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, March 18, 2013 10:35 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the fatal error. This error states that I have inserted topology section position_restraints in a wrong place. I checked again the itp files included in my top file. They are matched correctly! Did I modified the settings incorrectly? What would be other potent problems? Please help me. Thanks for your help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, March 17, 2013 5:19 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/17/13 6:50 AM, Shima Arasteh wrote: Thanks for your replies. As you suggested, I did as follows: 1. made index groups of two chains of my protein 2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -n index-chain.ndx 3.Next, I included the itp files as follow in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef DPOSRE #include chainA_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef DPOSRE #include chainB_posre.itp #endif 4. I also added this line to my mdp file: define = -DPOSRE 5. In addition I added these at the top of itp files for bothe restrained chains: #ifdef DPOSRE #endif Now when I run the command : grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr I don't get any errors. But when I run the mdrun I don't see any position restraint terms in my log file. Would you please let me know your suggestions in this about? Did I do any steps by mistake? Yes, again there is a problem with the #ifdef statements. If you use: #ifdef DPOSRE ... #endif the corresponding define statement is -DDPOSRE. Think of the first D in the define statement as I am defining the following string to be true. Your .mdp file corresponds to the use of: #ifdef POSRE ... #endif -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: Fwd: [gmx-users] position restraints
Yes, I overcome the last problems and I could see the pos.rest energy term in my log file. In order to create the itp files to include in top file, I opened the gro file which I entered as an input in my mdrun command. How might I check this issue that all the atoms in itp groups are involved in position restraints? Is there any solutions to check it? Many many thanks for your replies Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 18, 2013 4:46 PM Subject: Re: Fw: Fwd: [gmx-users] position restraints On 3/18/13 6:02 AM, Shima Arasteh wrote: With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I don't know if this range of deviation with position restraints is sensible or not! I can't believe with such a force of 10 I still see deviations! I'd prefer to get less deviation. Would it be possible by using a greater fc ? Is it sensible? Were restraints correctly applied? Your last messages indicated fatal errors in trying to apply restraints - have you overcome those problems? Is there a position restraint energy term written to the .log and .edr files? Using such a huge force constant should not result in such RMSD values unless (1) they are not being applied or (2) whatever groups you have created for applying restraints do not cover all atoms that are being analyzed in the RMSD calculation, i.e. some are unrestrained and moving normally when you think they are being restrained. -Justin Thanks for your suggestions in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, March 16, 2013 12:24 AM Subject: Re: Fw: Fwd: [gmx-users] position restraints On 3/15/13 8:50 AM, Shima Arasteh wrote: Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? No, 0.2 nm is very high. With position restraints, offhand I would think around 0.05 nm or less would be indicative of proper restraints. This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Yes, using genrestr to create a suitable posre.itp file that includes only backbone atoms. -Justin Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: Fwd: [gmx-users] position restraints
On Mon, Mar 18, 2013 at 8:24 AM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Yes, I overcome the last problems and I could see the pos.rest energy term in my log file. In order to create the itp files to include in top file, I opened the gro file which I entered as an input in my mdrun command. How might I check this issue that all the atoms in itp groups are involved in position restraints? Is there any solutions to check it? The input coordinate file doesn't tell you anything. Load the trajectory and watch it. If atoms are moving that shouldn't be, you have a problem. Inspect the position restraint .itp file to see which atoms it covers, and cross-reference those with the chain topologies to make sure the atoms you think are being restrained actually are. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
Thanks for your replies. As you suggested, I did as follows: 1. made index groups of two chains of my protein 2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -n index-chain.ndx 3.Next, I included the itp files as follow in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef DPOSRE #include chainA_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef DPOSRE #include chainB_posre.itp #endif 4. I also added this line to my mdp file: define = -DPOSRE 5. In addition I added these at the top of itp files for bothe restrained chains: #ifdef DPOSRE #endif Now when I run the command : grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr I don't get any errors. But when I run the mdrun I don't see any position restraint terms in my log file. Would you please let me know your suggestions in this about? Did I do any steps by mistake? Thanks in advance. Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, March 16, 2013 4:06 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/16/13 8:34 AM, Shima Arasteh wrote: Thanks. As I understood from your emails, I need to make index groups of separate chains of my protein, use the index file in order to use in genrestr command and then include the specific itp files for each groups in top file? Do you mean this? Am I right? Yes. Try it. One more thing that I need to know is that how it is possible to make an index group except the options appear after running make index command? Type 'help' at the prompt or otherwise search gromacs.org and Google for example usage. It is very easy to create index groups specifying subsets of residues or just their backbone atoms, etc. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/17/13 6:50 AM, Shima Arasteh wrote: Thanks for your replies. As you suggested, I did as follows: 1. made index groups of two chains of my protein 2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -n index-chain.ndx 3.Next, I included the itp files as follow in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef DPOSRE #include chainA_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef DPOSRE #include chainB_posre.itp #endif 4. I also added this line to my mdp file: define = -DPOSRE 5. In addition I added these at the top of itp files for bothe restrained chains: #ifdef DPOSRE #endif Now when I run the command : grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr I don't get any errors. But when I run the mdrun I don't see any position restraint terms in my log file. Would you please let me know your suggestions in this about? Did I do any steps by mistake? Yes, again there is a problem with the #ifdef statements. If you use: #ifdef DPOSRE ... #endif the corresponding define statement is -DDPOSRE. Think of the first D in the define statement as I am defining the following string to be true. Your .mdp file corresponds to the use of: #ifdef POSRE ... #endif -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
As you said I changed define in mdp file to define=-DPOSRE . I also included backbone.itp file as this: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include backbone_posre.itp #endif ; Include POPC chain topology #include popc.itp ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 19936 CL 2 But I get this fatal error that my include part for position restraints is not correct: Fatal error: [ file backbone_posre.itp, line 79 ]: Atom index (364) in position_restraints out of bounds (1-360). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please give me suggestions? Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, March 16, 2013 12:25 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/15/13 9:43 AM, Shima Arasteh wrote: I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include strong_posre.itp #include backbone_posre.itp #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
As you said I changed define in mdp file to define=-DPOSRE . I also included backbone.itp file as this: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include backbone_posre.itp #endif ; Include POPC chain topology #include popc.itp ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 19936 CL 2 But I get this fatal error that my include part for position restraints is not correct: Fatal error: [ file backbone_posre.itp, line 79 ]: Atom index (364) in position_restraints out of bounds (1-360). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please give me suggestions? Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, March 16, 2013 12:25 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/15/13 9:43 AM, Shima Arasteh wrote: I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include strong_posre.itp #include backbone_posre.itp #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: As you said I changed define in mdp file to define=-DPOSRE . I also included backbone.itp file as this: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include backbone_posre.itp #endif ; Include POPC chain topology #include popc.itp ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 POPC238 SOL19936 CL2 But I get this fatal error that my include part for position restraints is not correct: Fatal error: [ file backbone_posre.itp, line 79 ]: Atom index (364) in position_restraints out of bounds (1-360). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please give me suggestions? The error message already did... Your chains are not identical. You are applying the same position restraints file to them. GROMACS doesn't know what you mean. Mark Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, March 16, 2013 12:25 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/15/13 9:43 AM, Shima Arasteh wrote: I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include strong_posre.itp #include backbone_posre.itp #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? It would not be possible because I don't see any option for seperate chains when running genrestr command. Thanks in advance. Sincerely, Shima From: Mark Abraham mark.j.abra...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, March 16, 2013 2:21 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: As you said I changed define in mdp file to define=-DPOSRE . I also included backbone.itp file as this: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include backbone_posre.itp #endif ; Include POPC chain topology #include popc.itp ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 19936 CL 2 But I get this fatal error that my include part for position restraints is not correct: Fatal error: [ file backbone_posre.itp, line 79 ]: Atom index (364) in position_restraints out of bounds (1-360). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please give me suggestions? The error message already did... Your chains are not identical. You are applying the same position restraints file to them. GROMACS doesn't know what you mean. Mark Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, March 16, 2013 12:25 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/15/13 9:43 AM, Shima Arasteh wrote: I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include strong_posre.itp #include backbone_posre.itp #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 7:09 AM, Shima Arasteh wrote: Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? It would not be possible because I don't see any option for seperate chains when running genrestr command. You need to provide a sensible index group to genrestr to create such groups. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
Thanks. As I understood from your emails, I need to make index groups of separate chains of my protein, use the index file in order to use in genrestr command and then include the specific itp files for each groups in top file? Do you mean this? Am I right? One more thing that I need to know is that how it is possible to make an index group except the options appear after running make index command? Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, March 16, 2013 3:39 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/16/13 7:09 AM, Shima Arasteh wrote: Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? It would not be possible because I don't see any option for seperate chains when running genrestr command. You need to provide a sensible index group to genrestr to create such groups. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 8:34 AM, Shima Arasteh wrote: Thanks. As I understood from your emails, I need to make index groups of separate chains of my protein, use the index file in order to use in genrestr command and then include the specific itp files for each groups in top file? Do you mean this? Am I right? Yes. Try it. One more thing that I need to know is that how it is possible to make an index group except the options appear after running make index command? Type 'help' at the prompt or otherwise search gromacs.org and Google for example usage. It is very easy to create index groups specifying subsets of residues or just their backbone atoms, etc. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Fw: Fwd: [gmx-users] position restraints
Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include strong_posre.itp #include backbone_posre.itp #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: Fwd: [gmx-users] position restraints
On 3/15/13 8:50 AM, Shima Arasteh wrote: Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? No, 0.2 nm is very high. With position restraints, offhand I would think around 0.05 nm or less would be indicative of proper restraints. This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Yes, using genrestr to create a suitable posre.itp file that includes only backbone atoms. -Justin Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/15/13 9:43 AM, Shima Arasteh wrote: I also included the position restraints as follows in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include backbone_posre.itp #include strong_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include strong_posre.itp #include backbone_posre.itp #endif As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively? It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your topology, what you need is -DPOSRE. It is very easy to tell when position restraints are being applied. A position restraint energy term is written to the .log and .edr files. If it's not there, you're not applying restraints. -Justin Thanks in advance. Your suggestions would be appreciated. Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) Subject: Fw: Fwd: [gmx-users] position restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Dear users, Although I put the position restraints on backbone, I get RMSD around 0.2 nm. Is it usual? This deviation is just for a minimization step only. I' m on doubt about keeping the backbone in a fix secondary structure. I' d prefer to restraint the backbone completely. Is it possible? Thanks in advance. Restraints allow, by definition, for slight deviations. Erik * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position restraints
Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Restraints allow, by definition, for slight deviations. Erik On Mar 14, 2013, at 12:51 PM, Shima Arasteh wrote: Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position restraints in SMD
Hi all, It may be naive but I would like to get some clear explanation in SMD ( COM pulling) reg. The question is, Before performing the COM-pulling (incase of protein ligand complex) do we need to position restrain the ligand using genrestr and then add the topology to the topol.top file. If not why should not we restrain the ligand. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/position-restraints-in-SMD-tp4999444.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints in SMD
On 7/16/12 5:36 AM, Raj wrote: Hi all, It may be naive but I would like to get some clear explanation in SMD ( COM pulling) reg. The question is, Before performing the COM-pulling (incase of protein ligand complex) do we need to position restrain the ligand using genrestr and then add the topology to the topol.top file. If not why should not we restrain the ligand. Thanks in advance The initial equilibration can be approached in a number of ways that includes restraining both the protein and ligand or one or the other. Restraints are only intended to avoid large structural changes due to reorganization of the solvent. Thus you may choose to restrain the whole complex initially and then reduce or remove the restraints over the course of further equilibration. There are no hard and fast rules. Look into the literature and see what others recommend, and evaluate for yourself whether or not such a protocol is reasonable in your case. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position Restraints of one of the moleculetpye
Ok. My topology: ; Include forcefield parameters #include ./charmm27.ff/forcefield.itp ; Include ligand topology #include ligand1.itp ; Include Position restraint file #ifdef POSRES_1 #include posre_ligand1.itp #endif ; Include ligand topology #include ligand2.itp ; Include Position restraint file #ifdef POSRES_2 #include posre_ligand2.itp #endif ; Include ligand topology #include ligand3.itp ; Include Position restraint file #ifdef POSRES_3 #include posre_ligand3.itp #endif ; Include ligand topology #include ligand4.itp ; Include Position restraint file #ifdef POSRES_4 #include posre_ligand4.itp #endif ; Include ligand topology #include ligand5.itp ; Include Position restraint file #ifdef POSRES_5 #include posre_ligand5.itp #endif ; Include ligand topology #include ligand6.itp ; Include Position restraint file #ifdef POSRES_6 #include posre_ligand6.itp #endif ; Include water topology #include ./charmm27mod.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include ./charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols ligand1 1 ligand2 1 ligand3 1 ligand4 1 ligand5 1 ligand6 1 SOL 4617 Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other information is the same posre_ligand1.itp - ... - posre_ligand2.itp are all the same files. Then when I grompp: Syntax error - File ligand2.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Any suggestions appreciated, Steven On Mon, May 28, 2012 at 5:25 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/28/12 10:48 AM, Steven Neumann wrote: Dear Gmx Users, I am fighting with the position restraints. My system cosnsists of 6 ligands - all of them have the same topology - ligand.itp. I want to: 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre ligand1.itp 2. Restrain 5 of them and pull one of them away. Here I came across some difficulties. I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp and by index files I create an index of the ligands I wan to restrain. Each my ligands has 46 atoms. When I process to grompp: Atom index (256) in position_restraints out of bounds (1-46). This probably means that you have inserted topology section position_restraints Shall I rename Ligands as different residue names? If my posre includes 1-46 atom all ligands are restraints? How to restrain just 5 out of 6 of them? Position restraints are applied on a per-moleculetype basis. If you have six copies of a ligand, the only way to do this is to define the sixth as a special [moleculetype] (even if it contains identical information) with a different name, such that it can be restrained in the absence of restraints on the others. See the logic here: http://www.gromacs.org/**Documentation/Errors#Atom_**index_n_in_position_* *restraints_out_of_boundshttp://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position Restraints of one of the moleculetpye
On 5/29/12 6:52 AM, Steven Neumann wrote: Ok. My topology: ; Include forcefield parameters #include ./charmm27.ff/forcefield.itp ; Include ligand topology #include ligand1.itp ; Include Position restraint file #ifdef POSRES_1 #include posre_ligand1.itp #endif ; Include ligand topology #include ligand2.itp ; Include Position restraint file #ifdef POSRES_2 #include posre_ligand2.itp #endif ; Include ligand topology #include ligand3.itp ; Include Position restraint file #ifdef POSRES_3 #include posre_ligand3.itp #endif ; Include ligand topology #include ligand4.itp ; Include Position restraint file #ifdef POSRES_4 #include posre_ligand4.itp #endif ; Include ligand topology #include ligand5.itp ; Include Position restraint file #ifdef POSRES_5 #include posre_ligand5.itp #endif ; Include ligand topology #include ligand6.itp ; Include Position restraint file #ifdef POSRES_6 #include posre_ligand6.itp #endif ; Include water topology #include ./charmm27mod.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include ./charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols ligand1 1 ligand2 1 ligand3 1 ligand4 1 ligand5 1 ligand6 1 SOL 4617 Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other information is the same posre_ligand1.itp - ... - posre_ligand2.itp are all the same files. Then when I grompp: Syntax error - File ligand2.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Any suggestions appreciated, Once you declare a [moleculetype], the other force field-level directives cannot be called. If all the ligand topologies are the same, remove [atomtypes] from all but the first. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position Restraints of one of the moleculetpye
On Tue, May 29, 2012 at 12:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/29/12 6:52 AM, Steven Neumann wrote: Ok. My topology: ; Include forcefield parameters #include ./charmm27.ff/forcefield.itp ; Include ligand topology #include ligand1.itp ; Include Position restraint file #ifdef POSRES_1 #include posre_ligand1.itp #endif ; Include ligand topology #include ligand2.itp ; Include Position restraint file #ifdef POSRES_2 #include posre_ligand2.itp #endif ; Include ligand topology #include ligand3.itp ; Include Position restraint file #ifdef POSRES_3 #include posre_ligand3.itp #endif ; Include ligand topology #include ligand4.itp ; Include Position restraint file #ifdef POSRES_4 #include posre_ligand4.itp #endif ; Include ligand topology #include ligand5.itp ; Include Position restraint file #ifdef POSRES_5 #include posre_ligand5.itp #endif ; Include ligand topology #include ligand6.itp ; Include Position restraint file #ifdef POSRES_6 #include posre_ligand6.itp #endif ; Include water topology #include ./charmm27mod.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include ./charmm27.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols ligand1 1 ligand2 1 ligand3 1 ligand4 1 ligand5 1 ligand6 1 SOL 4617 Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other information is the same posre_ligand1.itp - ... - posre_ligand2.itp are all the same files. Then when I grompp: Syntax error - File ligand2.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Any suggestions appreciated, Once you declare a [moleculetype], the other force field-level directives cannot be called. If all the ligand topologies are the same, remove [atomtypes] from all but the first. -Justin Thanks Justin. Removing [pairtypes] and [atomtypes] from all but not the first helped. Steven -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Position Restraints of one of the moleculetpye
Dear Gmx Users, I am fighting with the position restraints. My system cosnsists of 6 ligands - all of them have the same topology - ligand.itp. I want to: 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre ligand1.itp 2. Restrain 5 of them and pull one of them away. Here I came across some difficulties. I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp and by index files I create an index of the ligands I wan to restrain. Each my ligands has 46 atoms. When I process to grompp: Atom index (256) in position_restraints out of bounds (1-46). This probably means that you have inserted topology section position_restraints Shall I rename Ligands as different residue names? If my posre includes 1-46 atom all ligands are restraints? How to restrain just 5 out of 6 of them? Best, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position Restraints of one of the moleculetpye
On 5/28/12 10:48 AM, Steven Neumann wrote: Dear Gmx Users, I am fighting with the position restraints. My system cosnsists of 6 ligands - all of them have the same topology - ligand.itp. I want to: 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre ligand1.itp 2. Restrain 5 of them and pull one of them away. Here I came across some difficulties. I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp and by index files I create an index of the ligands I wan to restrain. Each my ligands has 46 atoms. When I process to grompp: Atom index (256) in position_restraints out of bounds (1-46). This probably means that you have inserted topology section position_restraints Shall I rename Ligands as different residue names? If my posre includes 1-46 atom all ligands are restraints? How to restrain just 5 out of 6 of them? Position restraints are applied on a per-moleculetype basis. If you have six copies of a ligand, the only way to do this is to define the sixth as a special [moleculetype] (even if it contains identical information) with a different name, such that it can be restrained in the absence of restraints on the others. See the logic here: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Position Restraints
Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? Regards, Dariush -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position Restraints
On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? If molecules that should be restrained are moving inappropriately, then the restraints are not being replied properly in the topology. In the absence of more substantial information, there's nothing else that can be said. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position Restraints
Thanks dear Justin. No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run. I could see the Pos. Res. works in md.log file. Regards, Dariush On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? If molecules that should be restrained are moving inappropriately, then the restraints are not being replied properly in the topology. In the absence of more substantial information, there's nothing else that can be said. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position Restraints
On 4/26/12 1:59 PM, Dariush Mohammadyani wrote: Thanks dear Justin. No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run. I could see the Pos. Res. works in md.log file. Then I don't understand what the problem is. You'll have to describe what you're doing in greater detail. -Justin Regards, Dariush On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? If molecules that should be restrained are moving inappropriately, then the restraints are not being replied properly in the topology. In the absence of more substantial information, there's nothing else that can be said. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints problem
Hey :)
A sed oneliner to generate position_restraints for the first
moleculetype in a file, using an fc of 200:
sed -n -e '/\[ *atoms *\]/,/^ *\[/{/^\( *[0-9]\+\) .*/s//\1 1 200 200
200/p}' -e '/\[ *atoms *\]/i[ position_restraints ]' molecule.itp
Cheers,
Tsjerk
On Wed, Mar 28, 2012 at 3:33 PM, Jernej Zidar jernej.zi...@gmail.com wrote:
True. Even more so if the position restraints file can be generated with
basic Bash commands in under a minute.
Jernej
On 28. mar. 2012, at 20:16, gmx-users-requ...@gromacs.org wrote:
It's pretty rare to have more than a handful of [moleculetype] sections,
each of which would want customized [position_restraints]. pdb2gmx will
write all-heavy-atom [position_restraints] sections which serve most
purposes. It would not be hard to modify genrestr to be useful in the
general case, but until a developer needs it badly enough, it'll be a
low priority :-)
Mark
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints problem
On 28/03/2012 6:52 PM, Jernej Zidar wrote: Hi. After successfully importing a CHARMM-generated PDB file to GROMACS I set out to do some short simulations. While all calculations finished without a problem if everything but the water molecules were fixed. Removing the position restraints led to the system blowing up. Using J. Lemkul's tutorial suggestion I generated an index file selecting one lipid atom from sphingomyelin and one from cholesterol using make_ndx and the selection: a P | a O3 (alternatively I tried also 6 | 7 | 17 | 18 | a P | a O3). Any of the two selections selects only atoms from the lipid part of the system. After creating the index file I used genrestr to position restrain the movements of the selected atoms and obtain a position restrain ITP file. I included this ITP file at the end of the lipid topology ITP file as instructed on GROMACS' website. In the last step I edited the MDP file to use the position restraints file for some lipid atoms but something went wrong as GROMPP complains: Fatal error: [ file sys9-tmp-ions-mini-nofix-2-posre.itp, line 116 ]: Atom index (12014) in position_restraints out of bounds (1-11954). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Indeed, checking the lipid ITP file revealed there is no atom index 12014, yet there is an atom index 12014 (with the proper name) in the GRO file (that I used to create both the index and the restraints file) where all the atoms are listed. What have I done wrong? See the warning in genrestr -h. If all you're doing is adding a single atom of position restraint per moleculetype, you can do that by hand faster than using make_ndx and genrestr and adding the #include. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Position restraints problem
On Wed, Mar 28, 2012 at 16:17, gmx-users-requ...@gromacs.org wrote: See the warning in genrestr -h. If all you're doing is adding a single atom of position restraint per moleculetype, you can do that by hand faster than using make_ndx and genrestr and adding the #include. Mark This in turn means genrestr is useless if one has more than one molecule type. While I could set the restraints manually, doing it by hand is not really an option if one has more than 100 entries. Ah well, bash magic to the rescue. Thanks, Jernej Zidar For posterity reasons here's the warning: WARNING: position restraints only work for the one molecule at a time. Position restraints are interactions within molecules, therefore they should be included within the correct [ moleculetype ] block in the topology. Since the atom numbers in every moleculetype in the topology start at 1 and the numbers in the input file for genrestr number consecutively from 1, genrestr will only produce a useful file for the first molecule. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints problem
On 28/03/2012 7:39 PM, Jernej Zidar wrote: On Wed, Mar 28, 2012 at 16:17,gmx-users-requ...@gromacs.org wrote: See the warning in genrestr -h. If all you're doing is adding a single atom of position restraint per moleculetype, you can do that by hand faster than using make_ndx and genrestr and adding the #include. Mark This in turn means genrestr is useless if one has more than one molecule type. While I could set the restraints manually, doing it by hand is not really an option if one has more than 100 entries. Ah well, bash magic to the rescue. It's pretty rare to have more than a handful of [moleculetype] sections, each of which would want customized [position_restraints]. pdb2gmx will write all-heavy-atom [position_restraints] sections which serve most purposes. It would not be hard to modify genrestr to be useful in the general case, but until a developer needs it badly enough, it'll be a low priority :-) Mark Thanks, Jernej Zidar For posterity reasons here's the warning: WARNING: position restraints only work for the one molecule at a time. Position restraints are interactions within molecules, therefore they should be included within the correct [ moleculetype ] block in the topology. Since the atom numbers in every moleculetype in the topology start at 1 and the numbers in the input file for genrestr number consecutively from 1, genrestr will only produce a useful file for the first molecule. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints problem
True. Even more so if the position restraints file can be generated with basic Bash commands in under a minute. Jernej On 28. mar. 2012, at 20:16, gmx-users-requ...@gromacs.org wrote: It's pretty rare to have more than a handful of [moleculetype] sections, each of which would want customized [position_restraints]. pdb2gmx will write all-heavy-atom [position_restraints] sections which serve most purposes. It would not be hard to modify genrestr to be useful in the general case, but until a developer needs it badly enough, it'll be a low priority :-) Mark smime.p7s Description: S/MIME cryptographic signature -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position restraints on heavy atoms or all?
Hello all, I am using amber99SB to model an antibody with organic ligands. I know we could choose to restrain all atoms or only heavy atoms during the equilibration. But I wonder if this really matters for my system. As far as I know, equilibration is aimed at getting the temperature and pressure right, mainly for the solvent. And as long as we are going to do a 'real' MD production run without restraints, it should not matter too much how we restrained the antibody and ligands? I am not if I am right about this. Any suggestions? Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints on heavy atoms or all?
On 30/10/2011 11:04 AM, Yun Shi wrote: Hello all, I am using amber99SB to model an antibody with organic ligands. I know we could choose to restrain all atoms or only heavy atoms during the equilibration. But I wonder if this really matters for my system. As far as I know, equilibration is aimed at getting the temperature and pressure right, mainly for the solvent. And as long as we are going to do a 'real' MD production run without restraints, it should not matter too much how we restrained the antibody and ligands? Initial velocities are sampled from a theoretical distribution. Initial positions can be quite unphysical from whatever process created them - particularly hydrogen atoms. These can combine poorly in the absence of some sensible restraints. Only you can assess the quality of your input model. Mark I am not if I am right about this. Any suggestions? Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints
On 16/06/2011 11:54 AM, Tom Dupree wrote: Greetings all, I have run into a little bit of a problem. I am trying to simulate a hetro-dimer. Through previous work we have identified 302 C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our simulations using charmm which gave us a significant speed up in simulation time. My supervisor is keen for me to do a comparison of that method with a completely unrestrained system using the 53A6 FF. I managed to generate a position restraint file using the .gro file and genrestr. However when I get to the simulation step I can't get grompp to work. As genrestr -h will warn you, its output is only useful for the first molecule. GROMACS position restraints will not give you any implementation-related speed-up, only one from reducing the sampling volume. Freeze groups will give you some speed-up (at the cost of making your results depend on your frozen configuration), but you will usually not be able to use both constraints and NPT as well. I ran genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr Such a constraint or distance restraint matrix can only work intra-[moleculetype], and so is futile for your case. As I understand my situation grompp is looking for atom numbers in subset.itp and matching them to the atom numbers in topol_Protein_chain_x.itp and since the atom numbers in subset.itp are based on the em.gro file it fails/goes out of range. Yep Thanks to some chain breaks in my structure I have 6 chains instead of 2, is there a way convert the .gro numbers into the .itp numbers? and hence generate my restraint files based on the topol_Protein_chain_x.itp files? Sure, use editconf with some appropriate index groups (and maybe -resnr) to create subset structures that will then produce output from genrestr suitable for use with grompp. Furthermore can I actually do a constraint matrix over multiple molecules? Not without uniting the [moleculetypes]. Do note that the various kinds of restraints, constraints and freeze groups are all distinct approaches, and attempting to mix them can be asking for trouble. Be sure to use the right terminology when asking for help :-) Mark Or is there a better way of achieving my desired result? (302 atoms across 2 (6) chains constrained in their relative positions) All the best, Tom Fatal error: [ file subset.itp, line 145 ]: Atom index (5222) in constraints out of bounds (1-5149). This probably means that you have inserted topology section constraints in a part belonging to a different molecule than you intended to. In that case move the constraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My topology file ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue May 31 11:44:23 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include posre_Protein_chain_A.itp #endif #include topol_Protein_chain_A2.itp #ifdef POSRES #include posre_Protein_chain_A2.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include posre_Protein_chain_B.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B2.itp #ifdef POSRES #include posre_Protein_chain_B2.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B3.itp #ifdef POSRES #include posre_Protein_chain_B3.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B4.itp #ifdef POSRES #include posre_Protein_chain_B4.itp #endif #ifdef REST #include subset.itp #endif ___ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Position restraints with multiple identical molecules
Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include posre.itp #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading 91 1 2000 2000 2000 gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints with multiple identical molecules
Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include posre.itp #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading 91 1 2000 2000 2000 gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints with multiple identical molecules
You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin Hi Justin, thanks for your reply. If this is the case then should I not expect to see all the position restraints in the .tpr file? Using gmxdump -s md1.tpr to inspect the file I can only see Position Rest.: nr: 2 iatoms: 0 type=1 (POSRES) 0 (this is on the simplified 5 atom case). Which implies there is one position restraint on atom 1 (index 0 I guess). Craig Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include posre.itp #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading 91 1 2000 2000 2000 gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints with multiple identical molecules
Hi Justin, Ok - the .tpr file only lists the atoms from the molecule type. I get it now. Thanks again! Craig On 16 Jun 2011, at 12:58, Justin A. Lemkul wrote: Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp file and have placed: #ifdef POSRES #include posre.itp #endif in (hopefully) the correct part of the topology file (immediately below the only [moleculetype]). There are no solvent molecules or ions. Applying a position restraint to atom 91 works fine with posre.itp containing: [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 This results in just one restraint to atom 91. But if I want to restrain the 91st atom in the second molecule (atom 182 in the .gro file), how do I do it? You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that contains it, so if you only have one [moleculetype] then any instance of it will have the restraint applied to whatever atoms are indicated. -Justin [ position_restraints ] ; ai funct fc (in x, y and z) 91 1 2000 2000 2000 182 1 2000 2000 2000 Does not work since 182 is outside the atom numbers in the [moleculetype] (1 to 91). Similarly, having 32 lines in posre.itp reading 91 1 2000 2000 2000 gives 32 position restraints to atom 91. I expect I can get around this problem by duplicating the current topology 32 times and creating a huge topol.top file with all 2912 atoms defined explicitly. However, it seems there should be a more elegant way to achieve this. Any help would be greatly appreciated! I have included below a simplified example with all the other atoms removed. In this case, how do you restrain the position of atom 2,3,4 and 5? Craig Craig Kitchen Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK topol.top: [ moleculetype ] ; Atom ; Name nrexcl UNK 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 amber99_41 1 UNK OAI 1 -0.50762 15.9994 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name Multiple Atoms [ molecules ] ; Compound#mols UNK 5 Starting conf.gro: Multiple Atoms 5 1UNKOAI1 0.767 1.527 0.970 2UNKOAI2 0.988 0.716 1.774 3UNKOAI3 0.556 0.587 0.434 4UNKOAI4 0.335 1.656 2.436 5UNKOAI5 0.766 1.527 2.373 2.64620 3.76260 2.80720 File used for restraint coordinates (grompp -r) : Restraint coordinates 5 1UNKOAI1 0.000 1.500 1.000 2UNKOAI2 1.100 0.621 2.000 3UNKOAI3 0.399 0.621 0.349 4UNKOAI4 0.221 1.562 -0.343 5UNKOAI5 0.923 1.561 2.458 2.64620 3.76260 2.80720 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Position restraints
Greetings all, I have run into a little bit of a problem. I am trying to simulate a hetro-dimer. Through previous work we have identified 302 C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our simulations using charmm which gave us a significant speed up in simulation time. My supervisor is keen for me to do a comparison of that method with a completely unrestrained system using the 53A6 FF. I managed to generate a position restraint file using the .gro file and genrestr. However when I get to the simulation step I can't get grompp to work. I ran genrestr -f em.gro -n subset.ndx -o subset.itp -disre -constr As I understand my situation grompp is looking for atom numbers in subset.itp and matching them to the atom numbers in topol_Protein_chain_x.itp and since the atom numbers in subset.itp are based on the em.gro file it fails/goes out of range. Thanks to some chain breaks in my structure I have 6 chains instead of 2, is there a way convert the .gro numbers into the .itp numbers? and hence generate my restraint files based on the topol_Protein_chain_x.itp files? Furthermore can I actually do a constraint matrix over multiple molecules? Or is there a better way of achieving my desired result? (302 atoms across 2 (6) chains constrained in their relative positions) All the best, Tom Fatal error: [ file subset.itp, line 145 ]: Atom index (5222) in constraints out of bounds (1-5149). This probably means that you have inserted topology section constraints in a part belonging to a different molecule than you intended to. In that case move the constraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My topology file ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue May 31 11:44:23 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -f 3LP2.pdb -o 3lp2 -ignh -v ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include posre_Protein_chain_A.itp #endif #include topol_Protein_chain_A2.itp #ifdef POSRES #include posre_Protein_chain_A2.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include posre_Protein_chain_B.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B2.itp #ifdef POSRES #include posre_Protein_chain_B2.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B3.itp #ifdef POSRES #include posre_Protein_chain_B3.itp #endif #ifdef REST #include subset.itp #endif #include topol_Protein_chain_B4.itp #ifdef POSRES #include posre_Protein_chain_B4.itp #endif #ifdef REST #include subset.itp #endif ___ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Position restraints
Dear gmx-users, I am trying to simulate a thermalized wall in the framework of CG Martini force field. To do this I am planning to link my wall atoms to some reference points (initial positions) by harmonic potentials. From what I have found in the manual it looks like this can be done by using [position_restraints] declaration. What is not clear to me from the manual is if I understand correctly that as the reference position GROMACS will use the initial positions of the particles mentioned in [position_restraints] decraration? If yes then which positions of the wall particles will be written out at the end of the run? The initial ones (reference positions) or the instantaneous position of these particle at the end of the run? Many thanks in advance, Mikhail = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 6182 Fax:+966 3 330 0845 mstu...@slb.commailto:mstu...@slb.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position restraints
Mikhail Stukan wrote: Dear gmx-users, I am trying to simulate a thermalized wall in the framework of CG Martini force field. To do this I am planning to link my wall atoms to some reference points (initial positions) by harmonic potentials. From what I have found in the manual it looks like this can be done by using [position_restraints] declaration. What is not clear to me from the manual is if I understand correctly that as the “reference position” GROMACS will use the initial positions of the particles mentioned in [position_restraints] decraration? If yes then which positions of the Correct. wall particles will be written out at the end of the run? The initial ones (“reference positions”) or the instantaneous position of these particle at the end of the run? The instantaneous positions. Since the atoms can move using position restraints (with the amount controlled by the force constant specified), there is no guarantee that the positions will not change, and in fact, they usually do, even if the amount is very small. -Justin Many thanks in advance, Mikhail = Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 6182 Fax:+966 3 330 0845 mstu...@slb.com mailto:mstu...@slb.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints and out of bounds atom index
Since anybody helped me with this issue and I solved the problem, I'll report the solution here to contribute with the comunity. As I pointed in the original e-mail, the problem was the difference between the numbering scheme of .gro file and .itp file. I created 3 .pdb files, one for each chain and with pdb2gmx I created 3 .gro files. With these 3 .gro files I created 3 .ndx files with the groups I'd like to apply PR and from these .ndx files I created the PR .itp files, now with the numbering agreeing with the one of the topology files. The include of these PR.itp files in .top file is the same I mentioned in the original e-mail. With this, everything worked fine. Cheers ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** Em 16-10-2010 15:41, Alexandre Suman de Araujo escreveu: Hi all I'm trying to simulate a system with 3 chains (A, H and L). Pb2gmx gave me 3 .itp files (one for each chain), each one with atom number starting from 1, and a .top file with these 3 .itp included. It gave me also a .gro file with the 3 chains numbered consecutively (the atom number does not restart from 1 for each chain). With this .gro file I made an index file using make_ndx with 3 groups containing the backbone of each chain. With this index file I built 3 position restraint files with genrestr, one for each chain. Following the instructions from website, I removed the #ifdef POSRES/#include/#endif lines from the end of the .itp file of each chain and added them directly in the .top file as shown below: ; ;File 'proteina.gro.top' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Thu Oct 14 14:22:01 2010 ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.1 ; ;Command line was: ;pdb2gmx -f 2R29CL_original.pdb -o protein.gro -p proteina.gro -his -ignh ; ;Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp ; Include chain topologies #include proteina.gro_Protein_chain_A.itp ; Include Position restraint file for chain A #ifdef POSRES #include posre_Protein_chain_A.itp #endif #include proteina.gro_Protein_chain_H.itp ; Include Position restraint file for chain H #ifdef POSRES #include posre_Protein_chain_H.itp #endif #include proteina.gro_Protein_chain_L.itp ; Include Position restraint file for chain L #ifdef POSRES #include posre_Protein_chain_L.itp #endif ; Include water topology #include oplsaa.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include oplsaa.ff/ions.itp [ system ] ; Name ENVELOPE PROTEIN E; HEAVY CHAIN OF FAB 1A1D-2; LIGHT CHAIN OF FAB 1A1D-2 in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_H 1 Protein_chain_L 1 SOL59 SOL97 SOL95 SOL 30308 NA 91 CL 97 When I run a simulation without the define = -DPOSRES definition in the .mdp file, grompp runs ok. However, when I say in .mdp file to use position restraints grompp give me the following error: Fatal error: [ file posre_Protein_chain_H.itp, line 334 ]: Atom index (3221) in position_restraints out of bounds (1-3212). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I know that this was already discussed in list but nothing described there worked. It is clear that the problem is due to the different numbering scheme of the .gro file and .itp files. The .gro file does not restart the numbering scheme when a new chain starts, on the other hand, the .itp file of each chain starts from 1 in atom number field. Since the position restraint file is generated based on numbering scheme of the .gro file, in some cases (my case is one of them) the PR file refers to a atom number that does not exists in .itp file. I think the way to correct this was generate only one .itp file for
[gmx-users] position restraints and out of bounds atom index
Hi all I'm trying to simulate a system with 3 chains (A, H and L). Pb2gmx gave me 3 .itp files (one for each chain), each one with atom number starting from 1, and a .top file with these 3 .itp included. It gave me also a .gro file with the 3 chains numbered consecutively (the atom number does not restart from 1 for each chain). With this .gro file I made an index file using make_ndx with 3 groups containing the backbone of each chain. With this index file I built 3 position restraint files with genrestr, one for each chain. Following the instructions from website, I removed the #ifdef POSRES/#include/#endif lines from the end of the .itp file of each chain and added them directly in the .top file as shown below: ; ; File 'proteina.gro.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Oct 14 14:22:01 2010 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.1 ; ; Command line was: ; pdb2gmx -f 2R29CL_original.pdb -o protein.gro -p proteina.gro -his -ignh ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp ; Include chain topologies #include proteina.gro_Protein_chain_A.itp ; Include Position restraint file for chain A #ifdef POSRES #include posre_Protein_chain_A.itp #endif #include proteina.gro_Protein_chain_H.itp ; Include Position restraint file for chain H #ifdef POSRES #include posre_Protein_chain_H.itp #endif #include proteina.gro_Protein_chain_L.itp ; Include Position restraint file for chain L #ifdef POSRES #include posre_Protein_chain_L.itp #endif ; Include water topology #include oplsaa.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include oplsaa.ff/ions.itp [ system ] ; Name ENVELOPE PROTEIN E; HEAVY CHAIN OF FAB 1A1D-2; LIGHT CHAIN OF FAB 1A1D-2 in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_H 1 Protein_chain_L 1 SOL59 SOL97 SOL95 SOL 30308 NA 91 CL 97 When I run a simulation without the define = -DPOSRES definition in the .mdp file, grompp runs ok. However, when I say in .mdp file to use position restraints grompp give me the following error: Fatal error: [ file posre_Protein_chain_H.itp, line 334 ]: Atom index (3221) in position_restraints out of bounds (1-3212). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I know that this was already discussed in list but nothing described there worked. It is clear that the problem is due to the different numbering scheme of the .gro file and .itp files. The .gro file does not restart the numbering scheme when a new chain starts, on the other hand, the .itp file of each chain starts from 1 in atom number field. Since the position restraint file is generated based on numbering scheme of the .gro file, in some cases (my case is one of them) the PR file refers to a atom number that does not exists in .itp file. I think the way to correct this was generate only one .itp file for the 3 chains, or one .gro file for each chain and use them to create the PR .itp files. However, I don't know how to do any of these 2 tasks using pdb2gmx. Could anyone help me with this issue? There is any other program in Gromacs package that I should use to fix this problem? Best regards. -- Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Novo Webmail IFSC -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Position Restraints
Hi, When I used the genrestr to get the posre.itp specially, I found it set all atom to be applied to. Is that okay? How could I figure out which ones should not be set to. A little naive questions, but I do do not know. Thanks with regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Position Restraints
#ZHAO LINA# wrote: Hi, When I used the genrestr to get the posre.itp specially, I found it set all atom to be applied to. Is that okay? How could I figure out which ones should not be set to. A little naive questions, but I do do not know. The answer depends on your needs. When running genrestr without an index file, you can choose from any of the default groups. If you provide an index file, any group can be chosen. The default behavior of pdb2gmx is to generate a posre.itp file that restrains all heavy (non-H) atoms. You can do the same with genrestr if you want, but again, the atoms you want to restrain depend on your goals. -Justin Thanks with regards, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Position Restraints
Thanks for your answer. How can I tell which ones I should restrain? all no-H atoms? in most general situations. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, September 22, 2010 11:15 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Position Restraints #ZHAO LINA# wrote: Hi, When I used the genrestr to get the posre.itp specially, I found it set all atom to be applied to. Is that okay? How could I figure out which ones should not be set to. A little naive questions, but I do do not know. The answer depends on your needs. When running genrestr without an index file, you can choose from any of the default groups. If you provide an index file, any group can be chosen. The default behavior of pdb2gmx is to generate a posre.itp file that restrains all heavy (non-H) atoms. You can do the same with genrestr if you want, but again, the atoms you want to restrain depend on your goals. -Justin Thanks with regards, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Position Restraints
Thanks for your answer again. I will restrain the heavy atoms only first. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, September 22, 2010 11:43 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Position Restraints #ZHAO LINA# wrote: Thanks for your answer. How can I tell which ones I should restrain? all no-H atoms? in most general situations. For the sake of clarity in the archive, it's probably best to avoid broad generalizations. People can easily stumble upon a post and take it way out of context. A general situation might encompass a lot. I will reiterate that if you want to recapitulate the behavior of pdb2gmx with respect to typical biomolecules, you should choose all non-H atoms. If you have some other specialized application, I can make no recommendation, nor can anyone else, in the absence of a more thorough description. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, September 22, 2010 11:15 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Position Restraints #ZHAO LINA# wrote: Hi, When I used the genrestr to get the posre.itp specially, I found it set all atom to be applied to. Is that okay? How could I figure out which ones should not be set to. A little naive questions, but I do do not know. The answer depends on your needs. When running genrestr without an index file, you can choose from any of the default groups. If you provide an index file, any group can be chosen. The default behavior of pdb2gmx is to generate a posre.itp file that restrains all heavy (non-H) atoms. You can do the same with genrestr if you want, but again, the atoms you want to restrain depend on your goals. -Justin Thanks with regards, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position restraints
Hello, I would like to restrain my molecule to a specific position in space. I would like for certain atoms to lie on the y-axis. To do this I used the following code/lines in my .top file: [ position restraints ] 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; Unfortunately, after minimization my file contained the molecule in the same position as when the restraints were not applied. Does anyone know what I am doing wrong? Thanks in advance, Abdullah _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
abdullah ahmed wrote: Hello, I would like to restrain my molecule to a specific position in space. I would like for certain atoms to lie on the y-axis. To do this I used the following code/lines in my .top file: [ position restraints ] This is an incorrect directive. It should be position_restraints. 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; Unfortunately, after minimization my file contained the molecule in the same position as when the restraints were not applied. Does anyone know what I am doing wrong? Perhaps the directive name is an issue, although I think grompp should have raised a warning of some sort. Otherwise, is this block within the appropriate [moleculetype] in the topology? Is it under control of an #ifdef block that you haven't invoked in the .mdp file? -Justin Thanks in advance, Abdullah Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
FW: [gmx-users] position restraints
Thank you for your reply, I have been using [ position_restraints ], I do not know why it came out that way in the mail. I agree with you, the problem probably comes from the position the code lies in inside the .top file. I put it at the end of the file because I thought that was the way it was supposed to be done. Perhaps this is incorrect. The final lines of the .top file are: Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_A 1 [ position_restraints ] 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; Date: Thu, 3 Jun 2010 09:00:36 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] position restraints abdullah ahmed wrote: Hello, I would like to restrain my molecule to a specific position in space. I would like for certain atoms to lie on the y-axis. To do this I used the following code/lines in my .top file: [ position restraints ] This is an incorrect directive. It should be position_restraints. 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; Unfortunately, after minimization my file contained the molecule in the same position as when the restraints were not applied. Does anyone know what I am doing wrong? Perhaps the directive name is an issue, although I think grompp should have raised a warning of some sort. Otherwise, is this block within the appropriate [moleculetype] in the topology? Is it under control of an #ifdef block that you haven't invoked in the .mdp file? -Justin Thanks in advance, Abdullah Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
abdullah ahmed wrote: Thank you for your reply, I have been using [ position_restraints ], I do not know why it came out that way in the mail. I agree with you, the problem probably comes from the position the code lies in inside the .top file. I put it at the end of the file because I thought that was the way it was supposed to be done. Perhaps this is incorrect. That is incorrect. The position restraints must belong to the [moleculetype] of the species to be restrained. Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. Putting it at the very end of a file probably has no effect whatsoever on any of the species in your system. -Justin The final lines of the .top file are: Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_A 1 [ position_restraints ] 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; Date: Thu, 3 Jun 2010 09:00:36 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] position restraints abdullah ahmed wrote: Hello, I would like to restrain my molecule to a specific position in space. I would like for certain atoms to lie on the y-axis. To do this I used the following code/lines in my .top file: [ position restraints ] This is an incorrect directive. It should be position_restraints. 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; Unfortunately, after minimization my file contained the molecule in the same position as when the restraints were not applied. Does anyone know what I am doing wrong? Perhaps the directive name is an issue, although I think grompp should have raised a warning of some sort. Otherwise, is this block within the appropriate [moleculetype] in the topology? Is it under control of an #ifdef block that you haven't invoked in the .mdp file? -Justin Thanks in advance, Abdullah Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
FW: [gmx-users] position restraints
Hi! In your previous mail you mentioned: The position restraints must belong to the [moleculetype] of the species to be restrained. Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. So I rechecked my .top file and found that [moleculetype] only occurs once. Perhaps I have misunderstood you. So I added the top file below. I did not add the contents of [atoms] [bonds] etc because I felt the mail would become unnecessarily long. ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] [ bonds ] [ pairs ] [ angles ] [ dihedrals ] [ dihedrals ] ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_A 1 Thanks again for your help, Abdullah Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
abdullah ahmed wrote: Hi! In your previous mail you mentioned: The position restraints must belong to the [moleculetype] of the species to be restrained. * Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. * So I rechecked my .top file and found that [moleculetype] only occurs once. Perhaps I have misunderstood you. So I added the top file below. I No it doesn't. Each time you #include a new .itp file, you are telling grompp to copy and paste the contents of that .itp file in that location. Have a look at spc.itp - it starts a new moleculetype. http://www.gromacs.org/Documentation/Include_File_Mechanism Note how the automatically-generated posre.itp file is #included at the end of the Protein_A moleculetype, *before* any other molecules are introduced. You have to do the same with any new #include statements or directives you add. -Justin did not add the contents of [atoms] [bonds] etc because I felt the mail would become unnecessarily long. ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] [ bonds ] [ pairs ] [ angles ] [ dihedrals ] [ dihedrals ] ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_A 1 Thanks again for your help, Abdullah Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] position restraints
Hi, Sorry to bother you again, but I am new to gromacs and many theings don't make sense yet. I have tried reading the manual but I do not understand what you mean by Note how the automatically-generated posre.itp file is #included at the end of the Protein_A moleculetype, *before* any other molecules are introduced. You have to do the same with any new #include statements or directives you add. I tried using #include in front of my code for [position_restraints] but that just gives an error. So I suppose that isn't what you mean. Furthermore, in section 5.7.1 of the manual pg110 an example topology file called urea.top is shown. there is no include there. In this example .top file they just seem to have added the position restraints they want after the dihedrals. This approach does not seem to be working for me and I can not understand why. Thank you again for your help, Abdullah Date: Thu, 3 Jun 2010 09:43:18 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] position restraints abdullah ahmed wrote: Hi! In your previous mail you mentioned: The position restraints must belong to the [moleculetype] of the species to be restrained. * Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. * So I rechecked my .top file and found that [moleculetype] only occurs once. Perhaps I have misunderstood you. So I added the top file below. I No it doesn't. Each time you #include a new .itp file, you are telling grompp to copy and paste the contents of that .itp file in that location. Have a look at spc.itp - it starts a new moleculetype. http://www.gromacs.org/Documentation/Include_File_Mechanism Note how the automatically-generated posre.itp file is #included at the end of the Protein_A moleculetype, *before* any other molecules are introduced. You have to do the same with any new #include statements or directives you add. -Justin did not add the contents of [atoms] [bonds] etc because I felt the mail would become unnecessarily long. ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] [ bonds ] [ pairs ] [ angles ] [ dihedrals ] [ dihedrals ] ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_A 1 Thanks again for your help, Abdullah Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
Have you seen the example here? http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults What you need to do is place your [position_restraints] directive after the moleculetype to which it belongs, but before any other moleculetype has been introduced (usually by #including another topology, which introduces a new molecule, and hence, moleculetype). The example I mentioned regarding posre.itp is to demonstrate exactly how this is done. The posre.itp file is produced by pdb2gmx and is used to restrain the heavy atoms of the protein. It is #included (basically inserting the relevant [position_restraints] directive) at the end of the Protein_A moleculetype definition, but prior to the #include spc.itp statement, which starts the SPC water moleculetype definition. So the topology is like this: [ moleculetype ] Protein (atoms, bonds, other stuff...) [ position_restraints ] - Note how it is placed before the next moleculetype. [ moleculetype ] - This part comes from the #include spc.itp statement. SOL etc. -Justin abdullah ahmed wrote: Hi, Sorry to bother you again, but I am new to gromacs and many theings don't make sense yet. I have tried reading the manual but I do not understand what you mean by Note how the automatically-generated posre.itp file is #included at the end of the Protein_A moleculetype, *before* any other molecules are introduced. You have to do the same with any new #include statements or directives you add. I tried using #include in front of my code for [position_restraints] but that just gives an error. So I suppose that isn't what you mean. Furthermore, in section 5.7.1 of the manual pg110 an example topology file called urea.top is shown. there is no include there. In this example .top file they just seem to have added the position restraints they want after the dihedrals. This approach does not seem to be working for me and I can not understand why. Thank you again for your help, Abdullah Date: Thu, 3 Jun 2010 09:43:18 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] position restraints abdullah ahmed wrote: Hi! In your previous mail you mentioned: The position restraints must belong to the [moleculetype] of the species to be restrained. * Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. * So I rechecked my .top file and found that [moleculetype] only occurs once. Perhaps I have misunderstood you. So I added the top file below. I No it doesn't. Each time you #include a new .itp file, you are telling grompp to copy and paste the contents of that .itp file in that location. Have a look at spc.itp - it starts a new moleculetype. http://www.gromacs.org/Documentation/Include_File_Mechanism Note how the automatically-generated posre.itp file is #included at the end of the Protein_A moleculetype, *before* any other molecules are introduced. You have to do the same with any new #include statements or directives you add. -Justin did not add the contents of [atoms] [bonds] etc because I felt the mail would become unnecessarily long. ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Name nrexcl Protein_A 3 [ atoms ] [ bonds ] [ pairs ] [ angles ] [ dihedrals ] [ dihedrals ] ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_A 1 Thanks again for your help, Abdullah Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hotmail: Powerful
[gmx-users] Position restraints on a pentamer
Dear colleagues, I want to do MD simulation of only the extracellular domain of a pentamer, excluding the transmembrane domain. So, I want to restrain the part of the extracellular domain in contact with the transmembrane domain. I am using position restraints for few of those residues as well as to the two ends of one of the subunits, in which there are missing residues. [ position_restraints ] ; atom type fx fy fz 457 1 1000 1000 1000 459 1 1000 1000 1000 460 1 1000 1000 1000 461 1 1000 1000 1000 After few ns of MD, I observed that 3 of the subunits are distorted while the other 2 aren't. 1) Is this because of imposing position restraints or is it because of the gap between two subunits in on the subunits? 2)Is there any other way to restrain (apart from position restraints) the protein for this purpose? Coming to the missing residues part, I decided to use distance restraints between the two ends. Please note that only one of the chain is in covalently linked with the transmembrane domain. Rest of them have vanderwaals interactions. Thanks for any kind of suggestion in this regard. Prema. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Position restraints on a pentamer
Please ignore my previous mail. There was typo error. Dear colleagues, I want to do MD simulation of only the extracellular domain of a pentamer, excluding the transmembrane domain. So, I want to restrain the part of the extracellular domain in contact with the transmembrane domain. I am using position restraints for few of those residues as well as to the two ends of one of the subunits, in which there are missing residues. [ position_restraints ] ; atom type fx fy fz 457 1 1000 1000 1000 459 1 1000 1000 1000 460 1 1000 1000 1000 461 1 1000 1000 1000 After few ns of MD, I observed that 3 of the subunits are distorted while the other 2 aren't. 1) Is this because of imposing position restraints or is it because of the gap in between (due to missing residues) in one of the subunits? 2)Is there any other way to restrain (apart from position restraints) the protein for this purpose? Coming to the missing residues part, I decided to use distance restraints between the two ends. Please note that only one of the chain is in covalently linked with the transmembrane domain. Rest of them have vanderwaals interactions. Thanks for any kind of suggestion in this regard. Prema. - Original Message - From: [EMAIL PROTECTED] Date: Friday, August 15, 2008 2:00 pm Subject: Position restraints on a pentamer To: gmx-users@gromacs.org Dear colleagues, I want to do MD simulation of only the extracellular domain of a pentamer, excluding the transmembrane domain. So, I want to restrain the part of the extracellular domain in contact with the transmembrane domain. I am using position restraints for few of those residues as well as to the two ends of one of the subunits, in which there are missing residues. [ position_restraints ] ; atom type fx fy fz 457 1 1000 1000 1000 459 1 1000 1000 1000 460 1 1000 1000 1000 461 1 1000 1000 1000 After few ns of MD, I observed that 3 of the subunits are distorted while the other 2 aren't. 1) Is this because of imposing position restraints or is it because of the gap between two subunits in on the subunits? 2)Is there any other way to restrain (apart from position restraints) the protein for this purpose? Coming to the missing residues part, I decided to use distance restraints between the two ends. Please note that only one of the chain is in covalently linked with the transmembrane domain. Rest of them have vanderwaals interactions. Thanks for any kind of suggestion in this regard. Prema. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Position restraints on a pentamer
[EMAIL PROTECTED] wrote: Please ignore my previous mail. There was typo error. Dear colleagues, I want to do MD simulation of only the extracellular domain of a pentamer, excluding the transmembrane domain. So, I want to restrain the part of the extracellular domain in contact with the transmembrane domain. I am using position restraints for few of those residues as well as to the two ends of one of the subunits, in which there are missing residues. [ position_restraints ] ; atom type fx fy fz 457 1 1000 1000 1000 459 1 1000 1000 1000 460 1 1000 1000 1000 461 1 1000 1000 1000 After few ns of MD, I observed that 3 of the subunits are distorted while the other 2 aren't. Can you explain what you mean by distorted? Or post images online somewhere? 1) Is this because of imposing position restraints or is it because of the gap in between (due to missing residues) in one of the subunits? Potentially one or the other, or even both. In science, we have to eliminate variables, so you may want to try one of two things (if not both, ultimately): 1. Remove position restraints. 2. Fix the missing residues in the model. Depending on what you're interested in, either might be a viable option. I would think you'd like to rebuild the missing residues, unless you think they will have absolutely no effect on the dynamics. 2)Is there any other way to restrain (apart from position restraints) the protein for this purpose? There is an option within the .mdp file called freezegrps. Note that this option doesn't work well when applying pressure coupling. -Justin Coming to the missing residues part, I decided to use distance restraints between the two ends. Please note that only one of the chain is in covalently linked with the transmembrane domain. Rest of them have vanderwaals interactions. Thanks for any kind of suggestion in this regard. Prema. - Original Message - From: [EMAIL PROTECTED] Date: Friday, August 15, 2008 2:00 pm Subject: Position restraints on a pentamer To: gmx-users@gromacs.org Dear colleagues, I want to do MD simulation of only the extracellular domain of a pentamer, excluding the transmembrane domain. So, I want to restrain the part of the extracellular domain in contact with the transmembrane domain. I am using position restraints for few of those residues as well as to the two ends of one of the subunits, in which there are missing residues. [ position_restraints ] ; atom type fx fy fz 457 1 1000 1000 1000 459 1 1000 1000 1000 460 1 1000 1000 1000 461 1 1000 1000 1000 After few ns of MD, I observed that 3 of the subunits are distorted while the other 2 aren't. 1) Is this because of imposing position restraints or is it because of the gap between two subunits in on the subunits? 2)Is there any other way to restrain (apart from position restraints) the protein for this purpose? Coming to the missing residues part, I decided to use distance restraints between the two ends. Please note that only one of the chain is in covalently linked with the transmembrane domain. Rest of them have vanderwaals interactions. Thanks for any kind of suggestion in this regard. Prema. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: ...This usually means your system is exploding... Do you have any idea what may cause this problem? Not without further details. Where did you get the parameters for your lipid? What lipid is it? What did you do to minimize and equilibrate your system? What's in your .mdp file? See here: http://wiki.gromacs.org/index.php/blowing_up -Justin Hello, The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: title = TAT cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep dt = 0.002 ;ps nsteps = 400 nstlist = 10 ns_type = grid rlist = 0.99 coulombtype = PME rcoulomb = 0.99 vdwtype = cut-off rvdw = 0.99 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes emtol = 1000.0 emstep = 0.01 I tried running the steepest descent several times however that did not help. I run an MD simulation with the following parameters: title = dppc cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.001 ;ps nsteps = 10 nstcomm = 1 nstxout = 1000 nstvout = 0 nstfout = 0 nstenergy = 1000 nstlist = 10 pbc = no ns_type = simple rlist = 1.4 coulombtype = cut-off rcoulomb = 1.4 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = berendsen tau_t = 1.0 tc-grps = DPP ref_t = 300 Pcoupl = no gen_vel = yes gen_temp = 300.0 gen_seed = -1 bd_fric = 0 ld_seed = -1 epsilon_r = 80 comm_mode = angular thank you Gadi This message was sent using IMP, the Internet Messaging Program. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
[EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php This message was sent using IMP, the Internet Messaging Program. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php This message was sent using IMP, the Internet Messaging Program. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] position restraints
Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php This message was sent using IMP, the Internet Messaging Program. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080
Re: [gmx-users] position restraints
Quoting [EMAIL PROTECTED]: Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Basic information about this type of error can be found here (as well as several hundred posts in the list archive): http://wiki.gromacs.org/index.php/Errors#LINCS_warnings How did you do your minimization, with or without restraints? Did it converge to an acceptable potential energy? -Justin Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php This message was sent using IMP, the Internet Messaging Program. ___
Re: [gmx-users] position restraints
no prob you wait for some time it will write topology file and the proceed further.. On Thu, Apr 24, 2008 at 5:04 PM, [EMAIL PROTECTED] wrote: Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php This message was sent using IMP, the Internet Messaging Program. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please
Re: [gmx-users] position restraints
Quoting chandrabhan seniya [EMAIL PROTECTED]: no prob you wait for some time it will write topology file and the proceed further.. I think that a lipid molecule trying to tear itself apart at step 0 would fall under the category of a problem, and it will not disappear on it's own if we conveniently ignore it... On Thu, Apr 24, 2008 at 5:04 PM, [EMAIL PROTECTED] wrote: Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]
Re: [gmx-users] position restraints
chandrabhan seniya wrote: what is yr real prob tell me? On this list, we like constructive criticism. I don't think the above qualifies as such. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
