[gmx-users] Atoms are fused after inserting in membrane
Dear gromacs users I have prepared a complex system consists of a protein and carbohydrate in lipid membrane using the KALP-membrane tutorial. After concatenating the three coordinate files, I visualized using VMD, but around 18 lipid atoms and more than 25 water molecules are joined with my protein residues as well as carbohydrate. I proceed to energy minimization and it stops after reaching a step at ~500, showing high energy on one atom. My question is how to rectify this. I visualized using VMD and manually delete fused lipid and water molecule, but it creates large volume in membrane. I could not move forcefully because it disturb the conformation. Is any other way to correct it before proceeding to next phase. Thanks in advance, -Shine -- -- Shine Devaraj Assistant Professor Department of Biotechnology & Bioinformatics Dr. D Y Patil University, Navi Mumbai Associate Staff University of Central Lencashire, Preston, UK E:Mail: shinedev...@dypatil.edu,shin...@rediffmail.com Contact: (0)9320368486 Off: 022-39286142 -- 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] problem in converting coarse grained structure to fine strcture
>I used the command g_fg2cg to convert a coarse grained structure into >corresponding fine strcture, and i found that the water molecues can be >transformed correctly, but there is a big mess in the protien , and i could >not get correct protein strcture, can anyone give me some suggestion? g_fg2cg only generates an atomistic input structure for the actual reverse transformation run. The atoms are placed at random position within the CG-beads and thus the protein is supposed to be "a big mess" after this step. Please read "http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation"; for a more extensive explanation. Groetnis, Djurre -- 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] scaling factor for rna/dna
Hi, I suggest contacting people in Johan Åqvist's lab. I'm sure they know exactly what pitfalls there may be with regards to the choice of LIE parameters and what has been done for different types of molecules. Erik On 26 Mar 2013, at 02:42, Vishwambhar Bhandare wrote: > dear gromacs users, > I am doing LIE calculation in gromacs for RNA molecules, > What scaling factor (alpha and beta) should i use for calculation? > Is that default values for protein ligand will work'? > how we can get these alpha and beta scaling factors for nucleic acid? > thanks in advance.. > > > Thanks and Regards, > -- > Vishwambhar > Centre for Bioinformatics > Pondicherry University > Pondicherry > -- > > Note: Strictly confidential to Vishwayogi > -- > 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
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 To: Discussion list for GROMACS users 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] Atoms are fused after inserting in membrane
On 3/26/13 5:17 AM, Shine Devaraj wrote: Dear gromacs users I have prepared a complex system consists of a protein and carbohydrate in lipid membrane using the KALP-membrane tutorial. After concatenating the three coordinate files, I visualized using VMD, but around 18 lipid atoms and more than 25 water molecules are joined with my protein residues as well as carbohydrate. None of these molecules are "fused," but VMD thinks bonds exist because atoms are close together. I proceed to energy minimization and it stops after reaching a step at ~500, showing high energy on one atom. My question is how to rectify this. I visualized using VMD and manually delete fused lipid and water molecule, but it creates large volume in membrane. I could not move forcefully because it disturb the conformation. Is any other way to correct it before proceeding to next phase. You need to prepare the system more carefully. If you are following the protocol from my tutorial, then you've probably over-packed the lipids such that they get very close to the protein, though the outcome of the shrinking step energy minimizations should have made it obvious that something was wrong. As for the position of the carbohydrate, that's up to you to figure out. Water molecules also should not have gotten close to the protein or lipids if you use the approach described in the tutorial (increasing vdW radii to avoid solvation within the membrane). -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 To: Shima Arasteh ; Discussion list for GROMACS users 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
[gmx-users] About Deutrium Order Parameter
Dear Justin Thank you for your Previous reply, I want to calculate Variation of deuterium order Parameter With respect to Time for Entire Trajectory and Hydration Number of Phosphate oxygen For My Entire Trajectory . Thereby I can Identify the Equilibration Time For My Membrane Is There is Any Tool in gromacs? Thanks In advance -- 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: [gmx-users] About Deutrium Order Parameter
On 3/26/13 11:24 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply, I want to calculate Variation of deuterium order Parameter With respect to Time for Entire Trajectory and Hydration Number of Phosphate oxygen For My Entire Trajectory . Thereby I can Identify the Equilibration Time For My Membrane Is There is Any Tool in gromacs? I would suggest you consult the manual, Chapter 8 and Appendix D, where all the analysis tools are described in full. -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 wrote: > > > > 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: > ;pdb2
Re:Re: [gmx-users] problem in converting coarse grained structure to fine strcture
Dear Groetnis, Thank you very much for your nice suggestion. BW Fugui At 2013-03-26 17:34:08,"Djurre de Jong-Bruinink" wrote: >>I used the command g_fg2cg to convert a coarse grained structure into >>corresponding fine strcture, and i found that the water molecues can be >>transformed correctly, but there is a big mess in the protien , and i could >>not get correct protein strcture, can anyone give me some suggestion? > > >g_fg2cg only generates an atomistic input structure for the actual reverse >transformation run. The atoms are placed at random position within the >CG-beads and thus the protein is supposed to be "a big mess" after this step. > >Please read >"http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation"; >for a more extensive explanation. > > >Groetnis, >Djurre > >-- >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: Fw: [gmx-users] position restraints
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. 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!!! With these modifications, I got this top file: ; ; 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 . . . OBL OHL 1 0.28241489365 0.565258245152 OBL OSL 1 0.271724109033 0.45833423612 ; Different to C27 OBL OSLP 1 0.271724109033 0.45833423612 ; Not in C27 OBL NH3L 1 0.289542083396 0.648182492821 OBL NTL 1 0.289542083396 0.648182492821 OBL SL 1 0.311814551349 0.993644945843 OBL PL 1 0.316269044939 1.10856262394 ; ; Added new and changed old bonds/angles/dihedrals/impropers for CHARMM36 Lipids and also PS headgroup - Thomas Piggot July 2010 ; ; Also added in (but commented out) parameters for a trans double bond - TJP July 2010 ; [ bondtypes ] ; i j func b0 kb C HA 1 0.110 261568.824! FORM, formamide reverted to value from par_all22_prot.inp and par_cgenff_1d.inp CST OST 1 0.116 784884.928 SS FE 1 0.232 209200.0 C C 1 0.1335 502080.0 CA CA 1 0.1375 255224.0 . . . X FE NPH X 9 0.00 0.0 2 ; ### For Heme bound to HSD ; Charmm patch PHEM defines only one dihedral term: 1CD2 1NE2 2FE 2NA ; (1 = HSD, 2 = HEME) ; In gromacs we cannot differentiate between NA, NB, NC, and ND of the heme. ; (values cannot be attributed in the rtp file for dihedrals involving atoms ; from other residues) ; So we divide the original force constant (0.2092) by four. NPH FE NR2 CPH1 9 0.00 0.0 4 ; This one is always zero. NPH FE NR2 CPH2 9 0.00 0.0523 4 ; This is X-FE-NR2-X from charmm FE NR2 CPH1 X 9 0.00 0.0 1 FE NR2 CPH2 X 9 0.00 0.0 1 ; ### For Heme bound to O2 or CO, we dont have to do this trick, because the force constant is 0.0 X FE OM X 9 0.00 0.0 4 OM FE NR2 X 9 0.00 0.0 1 CM FE NR2 X 9 0.00 0.0 1 ; ### X NPH CPA X 9 0.00 0.0 2 X CTL1 OHL X 9 0.00 0.58576 3 X CTL2 OHL X 9 0.00 0.58576 3 X CTL3 OHL X 9 0.00 0.58576 3 . . . . X CEL1 CEL1 X 9 180.00 1.8828 1 ; New X CEL1 CEL1 X 9 180.00 35.564 2 X CEL2 CEL2 X 9 180.00 20.5016 2 [ dihedraltypes ] ; i j k l func q0 cq C NH1 O HA 2 0.00 66. ! J8_FVAL- , from CG2O1 NG2S2 OG2D1 HGR52, penalty= 1V CPB CPA NPH CPA 2 0. 174.0544 HA CPA CPA CPM 2 0. 246.0192 HE2 HE2 CE2 CE2 2 0.00 25.104 HR1 NR1 NR2 CPH2 2 0. 4.184 HR1 NR2 NR1 CPH2 2 0. 4.184 HR3 CPH1 NR1 CPH1 2 0. 4.184 HR3 CPH1 NR2 CPH1 2 0. 4.184 ; 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 curren
Re: Fw: [gmx-users] position restraints
On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh wrote: > 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 To: Discussion list for GROMACS users 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 wrote: > 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 wrote: > 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] Hydrophobic contact cut-off
Dear users, Sorry for an off-topic question.. What is the distance cut-off considered for hydrophobic contact in protein? Some paper states 4-8Ang, while some other considers only till 5Ang. It is reported that this is a long range interaction. Any information clarifying this doubt will be very useful. Thank you Kavya -- 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] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1
Dear Users: A cluster that I use went down today with a chiller failure. I lost all 16 jobs (running gromacs 4.6.1). For 13 of these jobs, not only is the .cpt file truncated, but also the _prev.cpt file is truncated, meaning that I am going to have to go back through the files, extract a frame, make a new .tpr file (using a new, custom .mdp file to get the timestamp right), restart the runs, and then later join the trajectory data fragments. I have experienced this a number of times over the years with different versions of gromacs (see, for example, http://redmine.gromacs.org/issues/790 ) and wonder if anybody else has experienced this? Also, does anybody have some advice on how to handle this? For now, my idea is to run a script in the background to periodically check the .cpt file and make a copy if it is not corrupted/truncated so that I can always restart. If it is useful information, both the .cpt and the _prev.cpt files have the same size and timestamp, but are smaller than non-corrupted .cpt files. E.g.: $ ls -ltr --full-time *cpt -rw-r- 1 cneale cneale 1963536 2013-03-22 17:18:04.0 -0700 md2d_prev.cpt -rw-r- 1 cneale cneale 1963536 2013-03-22 17:18:04.0 -0700 md2d.cpt -rw-r- 1 cneale cneale 1048576 2013-03-26 12:46:02.0 -0700 md3.cpt -rw-r- 1 cneale cneale 1048576 2013-03-26 12:46:03.0 -0700 md3_prev.cpt Where, above, md2d.cpt was from the last stage of my equilibration and md3.cpt was from my production. Here is another example from a different run with corruption: $ ls -ltr --full-time *cpt -rw-r- 1 cneale cneale 2209508 2013-03-21 08:24:33.0 -0700 md2d_prev.cpt -rw-r- 1 cneale cneale 2209508 2013-03-21 08:24:33.0 -0700 md2d.cpt -rw-r- 1 cneale cneale 2097152 2013-03-26 12:46:01.0 -0700 md3_prev.cpt -rw-r- 1 cneale cneale 2097152 2013-03-26 12:46:01.0 -0700 md3.cpt I detect corruption/truncation in the .cpt file like this: $ gmxcheck -f md3.cpt Fatal error: Checkpoint file corrupted/truncated, or maybe you are out of disk space? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Also, I confirmed the problem by trying to run mdrun: $ mdrun -nt 1 -deffnm md3 -cpi md3.cpt -nsteps 50 Fatal error: Checkpoint file corrupted/truncated, or maybe you are out of disk space? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors (and I get the same thing using md3_prev.cpt) I am not out of disk space, but probably some type of condition like that existed when the chiller failed and the system went down: $ df -h . FilesystemSize Used Avail Use% Mounted on 342T 57T 281T 17% /global/scratch Nor am I out of quota (although I have no command to show that here). There is no corruption of .edr, .trr, or .xtc files The .log files end like this: Writing checkpoint, step 194008250 at Tue Mar 26 10:49:31 2013 Writing checkpoint, step 194932330 at Tue Mar 26 11:49:31 2013 Step Time Lambda 195757661 391515.322000.0 Writing checkpoint, step 195757661 at Tue Mar 26 12:46:02 2013 I am motivated to help solve this problem, but have no idea how to stop gromacs from copying corrupted/truncated checkpoint files to _prev.cpt . I presume that one could write a magic number to the end of the .cpt file and test that it exists prior to moving .cpt to _prev.cpt , but perhaps I misunderstand the problem. If needs be, perhaps mdrun could call gmxcheck, since that tool seems to detect the corruption/truncation. If it's done every 30 minutes, it shouldn't affect the performance. Thank you for any advice, Chris. -- 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] Hydrophobic contact cut-off
The standard approach in cases like this, assuming that you have some contacts at some point in your trajectory, is to use your trajectory to construct a radial distribution function (RDF) and then to define a "contact" as any interaction up to the minimum following the first maximum of the RDF. This way, your cutoff will depend on your definition for contact evaluation (any atom pair, heavy atom pair, side chain center of mass, etc). Chris. -- original message -- Sorry for an off-topic question.. What is the distance cut-off considered for hydrophobic contact in protein? Some paper states 4-8Ang, while some other considers only till 5Ang. It is reported that this is a long range interaction. Any information clarifying this doubt will be very useful. Thank you Kavya -- 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] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1
Dear Chris, While it's always possible that GROMACS can be improved (or debugged), this smells more like a system-level problem. The corrupt checkpoint files are precisely 1MiB or 2MiB, which suggests strongly either 1) GROMACS was in the middle of a buffer flush when it was killed (but the filesystem did everything right; it was just sent incomplete data), or 2) the filesystem itself wrote a truncated file (but GROMACS wrote it successfully, the data was buffered, and GROMACS went on its merry way). #1 could happen, for example, if GROMACS was killed with SIGKILL while copying .cpt to _prev.cpt -- if GROMACS even copies, rather than renames -- its checkpoint files. #2 could happen in any number of ways, depending on precisely how your disks, filesystems, and network filesystems are all configured (for example, if a RAID array goes down hard with per-drive writeback caches enabled, or your NFS system is soft-mounted and either client or server goes down). With the sizes of the truncated checkpoint files being very convenient numbers, my money is on #2. Have you contacted your sysadmins to report this? They may be able to take some steps to try to prevent this, and (if this is indeed a system problem) doing so would provide all their users an increased measure of safety for their data. Cheers, MZ On Tue, Mar 26, 2013 at 10:04 PM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > Dear Users: > > A cluster that I use went down today with a chiller failure. I lost all 16 > jobs (running gromacs 4.6.1). For 13 of these jobs, not only is the .cpt > file truncated, but also the _prev.cpt file is truncated, meaning that I am > going to have to go back through the files, extract a frame, make a new > .tpr file (using a new, custom .mdp file to get the timestamp right), > restart the runs, and then later join the trajectory data fragments. > > I have experienced this a number of times over the years with different > versions of gromacs (see, for example, > http://redmine.gromacs.org/issues/790 ) and wonder if anybody else has > experienced this? > > Also, does anybody have some advice on how to handle this? For now, my > idea is to run a script in the background to periodically check the .cpt > file and make a copy if it is not corrupted/truncated so that I can always > restart. > > If it is useful information, both the .cpt and the _prev.cpt files have > the same size and timestamp, but are smaller than non-corrupted .cpt files. > E.g.: > > $ ls -ltr --full-time *cpt > -rw-r- 1 cneale cneale 1963536 2013-03-22 17:18:04.0 -0700 > md2d_prev.cpt > -rw-r- 1 cneale cneale 1963536 2013-03-22 17:18:04.0 -0700 > md2d.cpt > -rw-r- 1 cneale cneale 1048576 2013-03-26 12:46:02.0 -0700 > md3.cpt > -rw-r- 1 cneale cneale 1048576 2013-03-26 12:46:03.0 -0700 > md3_prev.cpt > > Where, above, md2d.cpt was from the last stage of my equilibration and > md3.cpt was from my production. > > Here is another example from a different run with corruption: > > $ ls -ltr --full-time *cpt > -rw-r- 1 cneale cneale 2209508 2013-03-21 08:24:33.0 -0700 > md2d_prev.cpt > -rw-r- 1 cneale cneale 2209508 2013-03-21 08:24:33.0 -0700 > md2d.cpt > -rw-r- 1 cneale cneale 2097152 2013-03-26 12:46:01.0 -0700 > md3_prev.cpt > -rw-r- 1 cneale cneale 2097152 2013-03-26 12:46:01.0 -0700 > md3.cpt > > I detect corruption/truncation in the .cpt file like this: > $ gmxcheck -f md3.cpt > Fatal error: > Checkpoint file corrupted/truncated, or maybe you are out of disk space? > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Also, I confirmed the problem by trying to run mdrun: > > $ mdrun -nt 1 -deffnm md3 -cpi md3.cpt -nsteps 50 > Fatal error: > Checkpoint file corrupted/truncated, or maybe you are out of disk space? > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > (and I get the same thing using md3_prev.cpt) > > I am not out of disk space, but probably some type of condition like that > existed when the chiller failed and the system went down: > $ df -h . > FilesystemSize Used Avail Use% Mounted on > 342T 57T 281T 17% /global/scratch > > Nor am I out of quota (although I have no command to show that here). > > There is no corruption of .edr, .trr, or .xtc files > > The .log files end like this: > > Writing checkpoint, step 194008250 at Tue Mar 26 10:49:31 2013 > Writing checkpoint, step 194932330 at Tue Mar 26 11:49:31 2013 >Step Time Lambda > 195757661 391515.322000.0 > Writing checkpoint, step 195757661 at Tue Mar 26 12:46:02 2013 > > I am motivated to help solve this problem, but have no idea how to stop > gromacs from copying corrupted/truncated checkpoint files to _prev.cpt .
[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1
Dear Matthew: Thank you for noticing the file size. This is a very good lead. I had not noticed that this was special. Indeed, here is the complete listing for truncated/corrupt .cpt files: -rw-r- 1 cneale cneale 1048576 Mar 26 18:53 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:54 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:54 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:54 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:50 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:50 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:50 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:51 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:51 md3.cpt -rw-r- 1 cneale cneale 2097152 Mar 26 18:52 md3.cpt -rw-r- 1 cneale cneale 2097152 Mar 26 18:52 md3.cpt -rw-r- 1 cneale cneale 2097152 Mar 26 18:52 md3.cpt -rw-r- 1 cneale cneale 2097152 Mar 26 18:52 md3.cpt I will contact my sysadmins and let them know about your suggestions. Nevertheless, I respectfully reject the idea that there is really nothing that can be done about this inside gromacs. About 6 years ago, I worked on a cluster with massive sporadic NSF delays. The only solution to automate runs on that machine was to, for example, use sed to create a .mdp from a template .mdp file, which had ;;;EOF as the last line and then to poll the created mdp file for ;;;EOF until it existed prior to running grompp (at the time I was using mdrun -sort and desorting with an in-house script prior to domain decomposition, so I had to stop/start gromacs every coupld of hours). This is not to say that such things are ideal, but I think gromacs would be all the better if it was able to avoid with problems like this regardless of the cluster setup. Please note that, over the years, I have seen this on 4 different clusters (albeit with different versions of gromacs), but that is to say that it's not just one setup that is to blame. Matthew, please don't take my comments the wrong way. I deeply appreciate your help. I just want to put it out there that I believe that gromacs would be better if it didn't overwrite good .cpt files with truncated/corrupt .cpt files ever, even if the cluster catches on fire or the earth's magnetic field reverses, etc. Also, I suspect that sysadmins don't have a lot of time to test their clusters for graceful exit upon chiller failure conditions, so a super-careful regime of .cpt update will always be useful. Thank you again for your help, I'll take it to my sysadmins, who are very good and may be able to remedy this on their cluster, but who knows what cluster I will be using in 5 years. Again, thank you for your assistance, it is very useful, Chris. -- original message -- Dear Chris, While it's always possible that GROMACS can be improved (or debugged), this smells more like a system-level problem. The corrupt checkpoint files are precisely 1MiB or 2MiB, which suggests strongly either 1) GROMACS was in the middle of a buffer flush when it was killed (but the filesystem did everything right; it was just sent incomplete data), or 2) the filesystem itself wrote a truncated file (but GROMACS wrote it successfully, the data was buffered, and GROMACS went on its merry way). #1 could happen, for example, if GROMACS was killed with SIGKILL while copying .cpt to _prev.cpt -- if GROMACS even copies, rather than renames -- its checkpoint files. #2 could happen in any number of ways, depending on precisely how your disks, filesystems, and network filesystems are all configured (for example, if a RAID array goes down hard with per-drive writeback caches enabled, or your NFS system is soft-mounted and either client or server goes down). With the sizes of the truncated checkpoint files being very convenient numbers, my money is on #2. Have you contacted your sysadmins to report this? They may be able to take some steps to try to prevent this, and (if this is indeed a system problem) doing so would provide all their users an increased measure of safety for their data. Cheers, MZ -- 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] (no subject)
Hai I have done 10ns simulation for a protein to this i want to calculate DCCM map.can you please suggest me how to calculate this map. Thank You. -- 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] Nose-hoover chains thermostat
Dear Gromacs Users! Could someone provide me with the tutorial example with the algoritm of ussing Nose-Hover chains thermostat. In particular It's not quite understood for me how I should define number of chains in the mdp file and how that number would affect on simulation performance (E.g In literatute I found that infinite chain number should give me maximum degree of ergodicity for my trajectory assuming modelling in cannonical ensemble). James -- 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] Simulation membrane proteins in amber99 force field.
Dear Gromacs users! I'd like to perform MD simulation of the membrane protein parametrized in Amber99sb force field. Could you tell me what cut-off patterns should I use for such simulation ? James -- 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] calculating LJ
Hello gmx, I have LJ parameter value of C (epsilon = 0.0262 kcal/mol, sigma = 3.83) O (epsilon = 0.1591. sigma = 3.12) in charmm format and wants to use them in gromos43a1 or charmm27 force field in gromacs. Could you tell me how do i convert them to gromacs format? Any examples plz. Thanks in advance. -- 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
