Re: [gmx-users] Interaction energy
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... If yes, will this simulation take longer? Thank you 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] solvents in gmx
On 2011-10-17 22:58, Justin A. Lemkul wrote: Yao Yao wrote: Hi Gmxers, Is there a way I can check all the kinds of solvents in gromacs? Apart from water, ethanol, ..., are there any Glycerol, Treholose, There likely aren't many. Anything available would be in the force field subdirectory for whatever force field you want. Others may be available on the User Contributions section of the Gromacs website. -Justin We have just submitted a paper about organic liquids. We provide boxes for 146 liquids and corresponding topologies. The systems have been equilibrated using GAFF and OPLS/AA. You can find these boxes at http://virtualchemistry.org. Please check back later for information on the corresponding paper. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Simulation of membrane protein
Dear Justin, Indeed I didnt take into account square degree so all values presented in the tutorial exactly true so this was exactly my mistake. :( After some iterations I've obtained value for S per lipid beetween 0.65-0.71 A^2. This is the example of the system wich I've obtained after solvation and futher minimization. http://www.sendspace.com/file/h6urhq It looks good. :) By the way I'd like to know about correct value for the S per protein ? Where I can obtain such information for my protein ? ( e.g for big proteins such receptors and channels ) The error with GenBox was due to the big vdv R for the carbons. It's intresting that I couldnt increase this value mush as 1.2. But my finally system didnt consist of some water within the membrane so I supose that it's good. Now my system on the stage of the equilibtation so I have not any questions yet but I only wounder to know about teqnique of the force fied preparation for the membrane protein simulation. In this work I've done this step in accordance with the tutorial. On the last stage I've copied gromos53a6_lipid.ff directory in $GMXLIB so now I can use it in pdb2gmx for instance. But when I've tried to make gro and top files for my lipid.pdb via pdb2gmx I've obtained errors that Residue 'DPP' not found in residue topology database so I think that in addition to the operations wich I've already done I should also make some changes in the /gromos53a6_lipid.ff/aminoacids.hdb ./gromos53a6_lipid.ff/aminoacids.n.tdb ./gromos53a6_lipid.ff/aminoacids.c.tdb shouldn't I? Finally, I've heard that there are already pre-build force fields for the membrane smulation. E.g I've heard that there is some modified CHARMM ff wich gave good results in simulation. Do you know something about this? Thank you for your help, 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] some questions about calculation of dipole ACF
I have been performing MD simulation on electrolyte solution recently. And I want to calculate the dipoles between cation-anion pairs. But I have no clue how to achieve this by gromacs. I also want to know the algorithm for command g_dipole about how to cheat a system with both molecules and ions separately. Your advisements will be quite helpful Thank you very much!~ -- 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] High temperature Simulation
Hello, Thank you. I got the point but I have a doubt, equilibrate under NPT until the pressure and temperature are stable, then switch to NVT to eliminate the boiling issue, how exactly it will eliminate the boiling issue if we dont use higher pressure while equlibrating? (as you said that it is difficult to simulate at high pressure due to stability reasons.) Thank you With Regards 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] dihedral restraint violation output
Dear Gromacs users,I would like to ask how I could vizualise the violations of the dihedral restraints in detail, i.e., a list of all violations.As far as I know, there is nothing like g_disre for dihedrals, or ?Kind regardsMarkusSMS schreiben mit WEB.DE FreeMail - einfach, schnell undkostenguenstig. Jetzt gleich testen! http://f.web.de/?mc=021192 -- 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] Interaction energy
Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- 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] Simulation of membrane protein
James Starlight wrote: Dear Justin, Indeed I didnt take into account square degree so all values presented in the tutorial exactly true so this was exactly my mistake. :( After some iterations I've obtained value for S per lipid beetween 0.65-0.71 A^2. This is the example of the system wich I've obtained after solvation and futher minimization. http://www.sendspace.com/file/h6urhq It looks good. :) By the way I'd like to know about correct value for the S per protein ? Where I can obtain such information for my protein ? ( e.g for big proteins such receptors and channels ) Such information depends on whether there is experimental evidence for the protein you're looking for. The error with GenBox was due to the big vdv R for the carbons. It's intresting that I couldnt increase this value mush as 1.2. But my finally system didnt consist of some water within the membrane so I supose that it's good. Now my system on the stage of the equilibtation so I have not any questions yet but I only wounder to know about teqnique of the force fied preparation for the membrane protein simulation. In this work I've done this step in accordance with the tutorial. On the last stage I've copied gromos53a6_lipid.ff directory in $GMXLIB so now I can use it in pdb2gmx for instance. But when I've tried to make gro and top files for my lipid.pdb via pdb2gmx I've obtained errors that Residue 'DPP' not found in residue topology database so I think that in addition to the operations wich I've already done I should also make some changes in the /gromos53a6_lipid.ff/aminoacids.hdb ./gromos53a6_lipid.ff/aminoacids.n.tdb ./gromos53a6_lipid.ff/aminoacids.c.tdb shouldn't I? pdb2gmx is not suited for building topologies of multi-molecule, heterogeneous systems like solvated membranes. You may be able to get a topology, but it will be a redundant mess. Follow the protocol in the tutorial; it avoids these issues in the most streamlined way possible. If you need a topology of a new lipid, create an .rtp entry (if one does not exist already) and run pdb2gmx on a single lipid molecule. You can then #include the new .itp file in your system topology. Finally, I've heard that there are already pre-build force fields for the membrane smulation. E.g I've heard that there is some modified CHARMM ff wich gave good results in simulation. Do you know something about this? Various CHARMM parameter sets exist. CHARMM27 is built into the Gromacs 4.5.x series, and CHARMM36 is available from the User Contributions section of the website. -Justin Thank you for your help, James -- 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] High temperature Simulation
Kavyashree M wrote: Hello, Thank you. I got the point but I have a doubt, equilibrate under NPT until the pressure and temperature are stable, then switch to NVT to eliminate the boiling issue, how exactly it will eliminate the boiling issue if we dont use higher pressure while equlibrating? (as you said that it is difficult to simulate at high pressure due to stability reasons.) You should equilibrate under whatever the necessary conditions are, be it high pressure or not. Once the desired parameters have been achieved, then switch to NVT. Since the box is invariant in NVT, you don't have to worry about anything expanding. Please continue to search in the literature for finer methodology points. I'm certain these issues have been addressed in greater detail elsewhere. -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] Interaction energy
On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. So do you mean that that I should add my index file with grompp -f md.mdp -c npt.gro -n *index.ndx* -t npt.cpt -p topol.top -o md.tpr with specified groups in md.mdp file like they are specified in index file? :) Then just to mdrun -rerun -deffnm md2 Please, let me know whether I am correct or not. Steven If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- ==**== 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] High temperature Simulation
Ok Thanks. On Tue, Oct 18, 2011 at 4:41 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Hello, Thank you. I got the point but I have a doubt, equilibrate under NPT until the pressure and temperature are stable, then switch to NVT to eliminate the boiling issue, how exactly it will eliminate the boiling issue if we dont use higher pressure while equlibrating? (as you said that it is difficult to simulate at high pressure due to stability reasons.) You should equilibrate under whatever the necessary conditions are, be it high pressure or not. Once the desired parameters have been achieved, then switch to NVT. Since the box is invariant in NVT, you don't have to worry about anything expanding. Please continue to search in the literature for finer methodology points. I'm certain these issues have been addressed in greater detail elsewhere. -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] Interaction energy
Steven Neumann wrote: On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. So do you mean that that I should add my index file with grompp -f md.mdp -c npt.gro -n *index.ndx* -t npt.cpt -p topol.top -o md.tpr with specified groups in md.mdp file like they are specified in index file? :) Then just to mdrun -rerun -deffnm md2 Please, let me know whether I am correct or not. Yes. -Justin Steven If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- ==__== 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 listgmx-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
[gmx-users] RE:Interaction Energy
Message: 1 Date: Tue, 18 Oct 2011 06:41:55 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Interaction energy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e9d57f3.10...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- Dear Steven, I did the following, but like Justin mentioned the files get large. Basically, I made a very complex ndx file from the beggining. I have the whole proteins and peptides involved, then a series of loops, and protein minus loop, and then individual amino acids and protein minus the amino acids. Basically every time you make the ndx for a particular amino acid/chain/loop you also have to generate the ndx for the rest of your protein minus what you were looking at. Otherwise you run out of groups to assign, and will start getting residue or atom in multiple groups when it is referenced more than one time. This might not be necessary in your case, but lets you divie up energy contributions easier, although multiple re-runs using varied indexes might be necessary, ie for the sum total, then varied parts, etc... At least that is a suggestion from my experience.. Freundlichen Grüsse Stephan Watkins -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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] RE:Interaction Energy
On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: Message: 1 Date: Tue, 18 Oct 2011 06:41:55 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Interaction energy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e9d57f3.10...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- Dear Steven, I did the following, but like Justin mentioned the files get large. Basically, I made a very complex ndx file from the beggining. I have the whole proteins and peptides involved, then a series of loops, and protein minus loop, and then individual amino acids and protein minus the amino acids. Basically every time you make the ndx for a particular amino acid/chain/loop you also have to generate the ndx for the rest of your protein minus what you were looking at. Otherwise you run out of groups to assign, and will start getting residue or atom in multiple groups when it is referenced more than one time. This might not be necessary in your case, but lets you divie up energy contributions easier, although multiple re-runs using varied indexes might be necessary, ie for the sum total, then varied parts, etc... At least that is a suggestion from my experience.. Freundlichen Grüsse Stephan Watkins -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- 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 Thank you Stephan! I have faced the problem you mentioned: Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 3) So as I understood what you have written I should specify in my INDEX.ndx: [r_91] - residue 91 1 2 3 7 [Protein-r91] - Protein without residue 91 8 9 10 11... 382 [r_92] - resideu 92 8 9 10 11...17 [Protein-r92] - Protein without residue 92 1 2..7 18 19 20...38 etc. etc. And the same with ligands but substracting from my [System] group? Then [Ligand] - all Ligands atoms [Protein] - all Protein atoms [Water] - all Water atoms. Please let me whether I am correct. Did such simulation take much longer? I run 100ns simulations for 2 days on the cluster with specified energy groups for Protein and Ligand only. My system consists of app. 4000 atoms only (water+protein+ligands). Thank you, 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] RE:Interaction Energy
Steven Neumann wrote: On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs lloyd.ri...@gmx.ch mailto:lloyd.ri...@gmx.ch wrote: Message: 1 Date: Tue, 18 Oct 2011 06:41:55 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] Interaction energy To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4e9d57f3.10...@vt.edu mailto:4e9d57f3.10...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- Dear Steven, I did the following, but like Justin mentioned the files get large. Basically, I made a very complex ndx file from the beggining. I have the whole proteins and peptides involved, then a series of loops, and protein minus loop, and then individual amino acids and protein minus the amino acids. Basically every time you make the ndx for a particular amino acid/chain/loop you also have to generate the ndx for the rest of your protein minus what you were looking at. Otherwise you run out of groups to assign, and will start getting residue or atom in multiple groups when it is referenced more than one time. This might not be necessary in your case, but lets you divie up energy contributions easier, although multiple re-runs using varied indexes might be necessary, ie for the sum total, then varied parts, etc... At least that is a suggestion from my experience.. Freundlichen Grüsse Stephan Watkins -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Thank you Stephan! I have faced the problem you mentioned: Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 3) So as I understood what you have written I should specify in my INDEX.ndx: [r_91] - residue 91 1 2 3 7 [Protein-r91] - Protein without residue 91 8 9 10 11... 382 [r_92] - resideu 92 8 9 10 11...17 [Protein-r92] - Protein without residue 92 1 2..7 18 19 20...38 etc. etc. And the same with ligands but substracting from my [System] group? This is not a correct approach, per the fatal error. If you want to monitor energies involving different residues, the only requirement is that those residues be in their own distinct groups, i.e.: energygrps = r_91 r_92 r_93 ... Ligand The energy groups cannot be redundant. What Stephan was suggesting is that you cannot, for instance, specify: energygrps = Protein r_91 r_92 ... because Protein encompasses residues 91, 92, etc. You can, however, specify
[gmx-users] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials
hey guys, i'm a really confused at the moment. reading the gromacs manual 4.5.4 (GM) and the paper introducing GAFF did not provide insight into this issue which drives me crazy! maybe some advanced gromacs user can do so. up to now, i have simulated very few different systems using amber force fields and gromacs (4.0.7). assume you have simulated the global minimum conformation of some handsome molecule mol mainly consisting of a simple cyclic aliphatic structure (about 13 atoms long) containing a double bond resulting in an E-mol and Z-mol isomer. i know from radicalic interconversion experiments, that Z-mol is about 100.000 times likelier than E-mol (due to the cyclic structure). from the simulation, which i've performed in water as well as in vacuum, i find that my intramolecular LJ14 and Coul14 energies indeed reflect the experimental steady state distribution. LJ-SR and Coul-SR just show slight differences only for the isomers. now, in order to see, whether the high 14-difference is caused by solvent effects or not, i extracted several energies from the vacuum simulation (E-mol left and Z-mol right) allowing me additionally to extract the potential energy (as well as bonded terms) of the molecule under consideration only: 1 Bond 69.267.3 2 Angle 96.1104.9 3 Proper Dih.3.14.6 4 Ryckaert-Bell.63.9106.3 5 LJ-14 48.446.1 6 Coulomb-14 -1036.6-1065.3 7 LJ (SR) 20.619.1 8 Coulomb (SR) 555.9556.5 9 Potential -179.4-160.5 the potential energy (line 9) obviously equals the sum of all other terms (line 1-8) and reveals, in contrast to the Coulomb-14 (C14) term, a completely different steady state distribution of cis- and trans-mol. this is mainly due to the Ryckaert-Bellemans (RB) term. however, as i've understood from the GM, the RB potential for dihedrals is not incorporated by every force field because often, the periodic type is used instead. and indeed, when comparing the equations from the gromacs manual with the Wang-paper in jCompChem-2004 concerning GAFF, it seems neither GAFF uses RB. and here are my lovely questions: Q1 am i right with my assumption whether GAFF uses RB or not? if not, will someone please explain it to me in a few words? Q2 why does the md.edr file provide two different terms concerning the same thing (proper dihedrals): proper dihedrals and RB how can i interpret these values? GM says: With the periodic GROMOS potential a special 1-4 LJ-interaction must be included; with the Ryckaert-Bellemans potential for alkanes the 1-4 interactions must be excluded from the non-bonded list. Note: Ryckaert-Bellemans potentials are also used in e.g. the OPLS force field in combination with 1-4 interactions Q3 does anyone know, how this is handled in GAFF? Q4 does this mean i have to exclude 1-4 manually, after having parameterized my molecules using acpype (antechamber)? GM says: For alkanes, the following proper dihedral potential [RB] is often used Q5 what does it depend on, whether RB is used for alkanes or not? GM says: For third neighbors, the normal Lennard-Jones repulsion is sometimes still too strong, ... especially the case for carbon-carbon interactions in a cis-conformation ... for some of these interactions, the Lennard-Jones repulsion has been reduced in the GROMOS force field, which is implemented by keeping a separate list of 1-4 and normal Lennard-Jones parameters. In other force fields, such as OPLS [88], the standard Lennard-Jones parameters are reduced by a factor of two, ... Q6 how this is handled with GAFF in gromacs? Q7 in general, can i still trust the given energies as listed above and compare them quantitatively? the simulation should actually result in a favorable Z-mol (due to strain) and less favorable E-mol. are the force fields and simulation software able to capture these kind of differences concerning the steady-state distribution of cis/trans, when the respective potentials are modified in such various ways among the force fields? Q8 does anyone have an idea, how to perform the simulation and on which energy terms to concentrate in order to get reliable results? thanks in advance and sorry for the long text ... as i've already told you, i'm really confused. kind regards vedat durmaz -- 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] N-terminal PGLU and C-term amidation
Hello, I am new to gromacs. I am applying the pdb2gmx tool to a peptide that has an N-term pyroglutamate and a C-term amidation. The OPLS forcefield has an entry for PGLU. I used the -ter flag of pdb2gmx to define protonation states of the termini. While this works fine for the C-term (choosing 3:None) I run into trouble with the PGLU at the N-term. In my input pdb the nitrogen of PGLU is attached to CA, CD and one proton. However when prompted 'Select start terminus type for PGLU-1' there is no NH option. If I select 'None' I get Fatal error: There is a dangling bond at at least one of the terminal ends. If I chose NH2 I end up with too many protons at my N-terminus. If I leave out the -ter flag altogether I get problems with my C- terminus: Fatal error: atom C not found in building block 23NH2 while combining tdb and rtp. How would I solve this? Regards, Henry Henry Hocking, PhD Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht, The Netherlands Phone: +31-30-2532875 Fax: +31-30-253 7623 E-mail: h.g.hock...@uu.nl -- 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] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials
On 19/10/2011 12:34 AM, Vedat Durmaz wrote: hey guys, i'm a really confused at the moment. reading the gromacs manual 4.5.4 (GM) and the paper introducing GAFF did not provide insight into this issue which drives me crazy! maybe some advanced gromacs user can do so. up to now, i have simulated very few different systems using amber force fields and gromacs (4.0.7). Don't exclusively read documentation that doesn't match the version of the software. Things change. assume you have simulated the global minimum conformation of some handsome molecule mol mainly consisting of a simple cyclic aliphatic structure (about 13 atoms long) containing a double bond resulting in an E-mol and Z-mol isomer. i know from radicalic interconversion experiments, that Z-mol is about 100.000 times likelier than E-mol (due to the cyclic structure). Part of that will be energy-based (E-mol has higher intra-atomic repulsion), and part will be entropy-based (Z-mol has fewer available configurations), but apparently a 13-atom ring is large enough that we should see the former dominate. from the simulation, which i've performed in water as well as in vacuum, i find that my intramolecular LJ14 and Coul14 energies indeed reflect the experimental steady state distribution. Maybe that is just fortuitous. Force fields are not parameterized to necessarily be able to be decomposed in ways that correlate numbers with chemical intuition. In particular, there is a balance between 1-4 charge-charge interaction and 1-4 dihedral interaction which depends on how everything else is parameterized. LJ-SR and Coul-SR just show slight differences only for the isomers. now, in order to see, whether the high 14-difference is caused by solvent effects or not, Note that you can construct subsets from your water .tpr and .trr with tpbconv and trjconv, and then use mdrun -rerun on these existing configuration, rather than run a vacuum simulation that samples different space. i extracted several energies from the vacuum simulation (E-mol left and Z-mol right) allowing me additionally to extract the potential energy (as well as bonded terms) of the molecule under consideration only: I'm assuming these are post-equilibration average values over at least several nanoseconds. Otherwise they don't mean anything at all. 1 Bond 69.267.3 2 Angle 96.1104.9 3 Proper Dih.3.14.6 4 Ryckaert-Bell.63.9106.3 5 LJ-14 48.446.1 6 Coulomb-14 -1036.6-1065.3 7 LJ (SR) 20.619.1 8 Coulomb (SR) 555.9556.5 9 Potential -179.4-160.5 the potential energy (line 9) obviously equals the sum of all other terms (line 1-8) and reveals, in contrast to the Coulomb-14 (C14) term, a completely different steady state distribution of cis- and trans-mol. this is mainly due to the Ryckaert-Bellemans (RB) term. One could equally observe that the contribution to the wrong relative energy is about half due to the angle term and about half due to the sum of dihedral and 1-4 terms. Apparently your experimental results suggest the same relative stability trend should be seen with the vacuum and condensed-phase systems, however the parameters you are using for the simulation are optimized for the condensed phase, so it is far from clear that they will produce the correct ensemble. If you'd done the mdrun -rerun I suggested and produced numbers like the above, you'd have the problem that you'd have assumed that the solvent potential energy is identical in each case. however, as i've understood from the GM, the RB potential for dihedrals is not incorporated by every force field because often, the periodic type is used instead. and indeed, when comparing the equations from the gromacs manual with the Wang-paper in jCompChem-2004 concerning GAFF, it seems neither GAFF uses RB. and here are my lovely questions: Q1 am i right with my assumption whether GAFF uses RB or not? if not, will someone please explain it to me in a few words? Read the GAFF paper for what mathematical function should be used. GROMACS would then have the job of implementing that function, but it need not do so with one that is named the same way. In particular, before GROMACS 4.5, there was no way of implementing multiple periodic dihedral types on the same four atoms (as used by CHARMM and AMBER force fields), so these had to be combined into one equivalent RB form. Q2 why does the md.edr file provide two different terms concerning the same thing (proper dihedrals): proper dihedrals and RB how can i interpret these values? Your .top file has both types, and it seems the latter result from the above-mentioned combining. GM says: With the periodic GROMOS potential a special 1-4 LJ-interaction must be included; with the Ryckaert-Bellemans potential for alkanes the 1-4 interactions must be excluded from the
Re: [gmx-users] RE:Interaction Energy
On Tue, Oct 18, 2011 at 2:50 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs lloyd.ri...@gmx.ch mailto: lloyd.ri...@gmx.ch wrote: Message: 1 Date: Tue, 18 Oct 2011 06:41:55 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] Interaction energy To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org** Message-ID: 4e9d57f3.10...@vt.edu mailto:4e9d57f3.10...@vt.edu** Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Neumann wrote: On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energy and specify each of my residues in index files but it is not possible. Will you suggest how to do this? For such information, you have to specify these groups as energygrps in the .mdp file. You can rerun the trajectory using mdrun -rerun and a new .tpr file specifying these groups, but depending on the output frequency, the result may not be as accurate as you'd like. -Justin Thank you Justin. Now I have two groups sepcified in my mdp file: energygrps = Protein LIG How can I specify each residue of my protein separately and each ligand? In my md.gro file I have residues: 91GLY 92TYR . 161LIG 162LIG... Will it be correct like this energygrps = 91GLY 92 TYR ... 161LIG 162LIG... No. The names must correspond to valid groups in an index file. If yes, will this simulation take longer? Thank you Perhaps, but certainly your energy file will be considerably larger. -Justin Steven -- =**=== Dear Steven, I did the following, but like Justin mentioned the files get large. Basically, I made a very complex ndx file from the beggining. I have the whole proteins and peptides involved, then a series of loops, and protein minus loop, and then individual amino acids and protein minus the amino acids. Basically every time you make the ndx for a particular amino acid/chain/loop you also have to generate the ndx for the rest of your protein minus what you were looking at. Otherwise you run out of groups to assign, and will start getting residue or atom in multiple groups when it is referenced more than one time. This might not be necessary in your case, but lets you divie up energy contributions easier, although multiple re-runs using varied indexes might be necessary, ie for the sum total, then varied parts, etc... At least that is a suggestion from my experience.. Freundlichen Grüsse Stephan Watkins -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/**freephonehttp://www.gmx.net/de/go/freephone -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists Thank you Stephan! I have faced the problem you mentioned: Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 3) So as I understood what you have written I should specify in my INDEX.ndx: [r_91] - residue 91 1 2 3 7 [Protein-r91] - Protein without residue 91 8 9 10 11... 382 [r_92] - resideu 92 8 9 10 11...17 [Protein-r92] - Protein without residue 92 1 2..7 18 19 20...38 etc. etc. And the same with ligands but substracting from my [System] group? This is not a correct approach, per the fatal error. If you want to monitor energies involving different residues, the only requirement is that those
[gmx-users] About pair distribution function
Dear Gromacs user . Thanks for your previous eply I am using plumed gromacs . i would like to find out Hydrophobic interaction free energies . As stated in manual.i used COORD keyword which is based on the Switching function . But When i use the COORD option i need to properly Guess the Term MM,NN, R_0 D_0 . For that i had been advised to look at the pair distribution function of the two groups (among Which i want to calculate Hydrophobic energies, plumed 1-2-2 manual) Is ther is any way to calculate pair Distribution function through gromacs. .between two set of groups . 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] Link to Intel MKL (fftw) via cmake options
On 17.10.2011 05:18, Mark Abraham wrote: On 17/10/2011 7:04 AM, Mirco Wahab wrote: On 10/16/2011 2:25 PM, Mark Abraham wrote: On 15/10/2011 9:02 PM, Mirco Wahab wrote: On 10/15/2011 1:15 AM, Mark Abraham wrote: I use ... ... ... OK, I can understand that. But if the options (-mtune ***, -msse2) are not longer available with the actual free Intel Compiler suites, shouldn't the cmake definitions be adapted to this fact in order to avoid loads of compiler warnings? If someone can identify a way to detect old and new, free and non-free compiler suites then we might consider it. Reality is that GROMACS spends a heavy majority of its time in loops written mostly in assembly code (using SSE or SSE2 if applicable), or in the FFT library. Compiler performance makes a negligible contribution to performance of the rest, so it is really not worth while maintaining complex compiler tweaks. OK, I'll attach the error messages err.msg, 5.9 KB). - cmake version 2.8.3 - gcc 4.5.1 x64 (Linux) (20101208) With cmake 2.8.2 and icc 12.1.0 20110811 using the aforementioned flags, I get smooth installation of the git version of 4.5.5. Moreover, I don't even get .../build/src/gmxlib/CMakeFiles/CMakeRelink.dir being created. So I think there is something idiosyncratic about your tool chain that is at the root of this. I replicated the error on another machine and already answered this as a response to Szilárd. I really don't know what the reason is, maybe I'm doing something really wrong. The only ray of hope: w/autoconf, everything works fine, even giving one the subjective impression of 'closely controlling' the build process ;-) Thanks regards M. -- 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] calculation time
Dear users, Sometimes, in the end ( in production simulation), Gromacs doesn't show calculation/finish time on screen, why? How can we show it? Thanks in advance -- Ahmet YILDIRIM -- 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] Charmm27 ff for membrane protein simulation
Greetings! Recently I've found that Charmm27 ff is widely used for the simulation of the membrane proteins. I've tried to work with pure DPPC bilayer in pdb2grx and obtain that charm27 ff included in the Gromacs is lack for the parametries for the lipids. Could you tell me where I could obtain those parametries ( and tutorial of how it might be included in processing of lipids) or full functional charmm27 ff that already has pre-built those parametries? Thank you for help 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
Re: [gmx-users] Charmm27 ff for membrane protein simulation
James Starlight wrote: Greetings! Recently I've found that Charmm27 ff is widely used for the simulation of the membrane proteins. I've tried to work with pure DPPC bilayer in pdb2grx and obtain that charm27 ff included in the Gromacs is lack for the parametries for the lipids. Could you tell me where I could obtain those parametries ( and tutorial of how it might be included in processing of lipids) or full functional charmm27 ff that already has pre-built those parametries? Most of the common lipids are already present in lipids.rtp in charmm27.ff in Gromacs 4.5.x; if you are looking for lipids not present there, please be more specific as to what you need. The only membrane protein tutorial to my knowledge is my own. Dealing with CHARMM should be significantly easier, however, as no modification of the force field is necessary. Run pdb2gmx on a single lipid molecule, convert the .top to .itp (see the wiki) and #include it in the .top for your protein, just like in my tutorial. -Justin Thank you for help James -- 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] Charmm27 ff for membrane protein simulation
By default in the CHARMM27 force field files there is no DPPC, as this is made up from a combination of other entries in the rtp file (because this is the way it is done in the CHARMM program's files). If you wish to use DPPC you can construct yourself a complete DPPC rtp entry. To do this you it is probably easiest to duplicate the DMPC entry and add the corresponding atoms and bonds for two extra carbons in each tail. Alternatively you could use the CHARMM36 force field (available to download from the contributions section of the website), there should already be an entry for DPPC. Cheers Tom On 18/10/11 19:45, Justin A. Lemkul wrote: James Starlight wrote: Greetings! Recently I've found that Charmm27 ff is widely used for the simulation of the membrane proteins. I've tried to work with pure DPPC bilayer in pdb2grx and obtain that charm27 ff included in the Gromacs is lack for the parametries for the lipids. Could you tell me where I could obtain those parametries ( and tutorial of how it might be included in processing of lipids) or full functional charmm27 ff that already has pre-built those parametries? Most of the common lipids are already present in lipids.rtp in charmm27.ff in Gromacs 4.5.x; if you are looking for lipids not present there, please be more specific as to what you need. The only membrane protein tutorial to my knowledge is my own. Dealing with CHARMM should be significantly easier, however, as no modification of the force field is necessary. Run pdb2gmx on a single lipid molecule, convert the .top to .itp (see the wiki) and #include it in the .top for your protein, just like in my tutorial. -Justin Thank you for help James -- Dr Thomas Piggot University of Southampton, UK. -- 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] Energy Drift
I posted to the list a few days ago with an energy drift problem. Mark Abraham helpfully suggested using all-bonds rather than h-bonds which solved the problem. I'm now trying to understand quite why that helped so much. The simulation is a protein of about 5000 atoms using GBSA, a time step of 2 fs, and a cut-off of 1.6 for VdW, coulomb and GB. I've run energy drift simulations using the md integrator, with no thermostat, and using the ld integrator with a tau_t of 100. Simulations were run changing various parameters. The changes were: - dt reduced to 1.5 - dt reduced to 1.0 - cutoff increased to 2.0 - constraint changed from h-bonds to all-bonds Plot of the energy drifts can be seen at http://www.reynwar.net/ben/gromacs/energy_drift.png. Noticeable features are: - changing the time step makes no difference (in my last post I claimed it did, which is why you should make plots rather than eyeballing log files). - increasing the cut-off helps a lot. - changing constraint to all-bonds make a dramatic difference - using ld there is a downwards drift in the energy when using all-bonds constraint. The temperature is roughly 300 K and the set point is 400 K so this downwards drift seems unlikely to be due to coupling to the langevin thermostat. My questions are: - why does the all-bonds constraint help so much? - why doesn't moving to a smaller time step help with this? - what is the cause of the downwards drift when using ld with all-bonds? Cheers, Ben -- 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] Energy Drift
Ben Reynwar wrote: I posted to the list a few days ago with an energy drift problem. Mark Abraham helpfully suggested using all-bonds rather than h-bonds which solved the problem. I'm now trying to understand quite why that helped so much. The simulation is a protein of about 5000 atoms using GBSA, a time step of 2 fs, and a cut-off of 1.6 for VdW, coulomb and GB. I've run energy drift simulations using the md integrator, with no thermostat, and using the ld integrator with a tau_t of 100. Simulations were run changing various parameters. The changes were: - dt reduced to 1.5 - dt reduced to 1.0 - cutoff increased to 2.0 - constraint changed from h-bonds to all-bonds Plot of the energy drifts can be seen at http://www.reynwar.net/ben/gromacs/energy_drift.png. Noticeable features are: - changing the time step makes no difference (in my last post I claimed it did, which is why you should make plots rather than eyeballing log files). - increasing the cut-off helps a lot. - changing constraint to all-bonds make a dramatic difference - using ld there is a downwards drift in the energy when using all-bonds constraint. The temperature is roughly 300 K and the set point is 400 K so this downwards drift seems unlikely to be due to coupling to the langevin thermostat. My questions are: - why does the all-bonds constraint help so much? - why doesn't moving to a smaller time step help with this? - what is the cause of the downwards drift when using ld with all-bonds? I can offer a bit of general advice here, but no specific answers. Hopefully it helps. To get at the root cause of all of this, you should be analyzing individual energy components, not just the total energy. These will tell you which terms are systematically changing. In my experience with GB simulations, using anything other than infinite cutoffs (i.e. all-vs-all kernel) has resulted in unstable simulations. I don't mean that the simulations crash or anything, but the results are clearly incorrect. Stably folded proteins have drastically increased RMSD and lose their structure very easily. The effect is independent of the chosen force field. I would recommend always using infinite cutoffs for GB simulations. It may improve your situation. -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
[gmx-users] Gromacs versions 4.0.5 and 4.5.4
Dear All, I have a simulation set up for a mixture of carbon dioxide and water system which runs perfectly on Gromacs 4.0.5 version. I have run these simulations at different temperatures and pressures, from the same starting configuration and the simulation proceeds smoothly in the 4.0.5 version. However, when I use exactly the same files to run the simulation in 4.5.4 version, the system crashes and writes out several pdb files. I was wondering if there is anything specific that has been changed between the two versions. I have pasted the mdp file of the simulations below. Any input will be much appreciated. MDP File title = 100% occupancy CO2 hydrate ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step nsteps = 1500 ; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = ; write coords nstvout = ; write velocities nstlog = 25000; print to logfile nstenergy = 500 ; print energies xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type= grid ; pairlist method coulombtype= PME rvdw = 1.2 ; cut-off for vdw rcoulomb = 1.2 ; cut-off for coulomb rlist= 1.2 ; cut-off for coulomb DispCorr = EnerPres Tcoupl = Nose-Hoover ref_t = 270 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic; pressure geometry tau_p= 1.0 1.0; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 30.5 30.5 ; ref pressure gen_vel = yes ; generate initial vel gen_temp = 260 ; initial temperature gen_seed = 372340 ; random seed constraint_algorithm = shake constraints = all-bonds --- Thank you, Sincerely, Sapna -- 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] reg g_rdf
Dear justin, Thanks for your replies. i am doing Steered MD .. i would like to calculate radial Distribution function. of Moving group with respect to Fixed group . I am pulling only in Z direction then is it possible to calculate RDF along Z-direction. only . it means Is there is any option in g_rdf tools of gromacs Available? 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] Gromacs versions 4.0.5 and 4.5.4
HiSapna,I had the same problem few weeks ago.Apparently, some parameters are different (eg.nstpcouple).Cheers,ItamarPSI found out that I prefer to stick to 4.0.7.---BeginMessage--- That seems possible Mark. I had actually assumed that Itamar extracted a .gro from the 4.0.7 simulations and created a new .tpr with 4.5.4 grompp. If that was the case, then I would still be surprised that it had instability problems. One sees a lot of charmm papers where people do slow heating, but my experience with gromacs is that not too many people worry about maintaining the velocities from their NVT simulations for their NPT simulations (or restrained - unrestrained) and that it works out just fine. On the other hand, I don't see too many gromacs reaction field studies either, so perhaps it all makes sense to those who use these methods. Thanks again, Chris. On 2/09/2011 12:59 AM, chris.neale at utoronto.ca wrote: That all makes sense Tsjerk. I wonder if mdrun terminations based on LINCS warnings should come with an additional message to explain that one may try running for a while with nstpcouple=1. That tip might be a good thing for the wiki page on that. Also, I'm still a little curious about a question that Itamar asked a few posts ago: If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? Mark provided a good explanation about how this could be possible, but I've never seen lincs warnings or systems blowing up after 5 ns of equilibration. I fully realize that it may take even us of simulation to properly equilibrate statistical properties, but in my experience it is far outside of ordinary to require 5 ns of equilibration to avoid systems blowing up. It's hard to say without more detail of how the extension occurred, and knowing how much ensemble data got lost. It's still conceivable some horrible mismatch occurred (e.g. virial over-written by some other data), but not really worth exploring properly. I'd just expect to have to re-equilibrate upon changing code version, and just not attempt such an extension. Mark Chris. -- original message -- Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rendering such simulations less stable. As for SD, probably that causes sufficient damping of jitter introduced due to pressure coupling for it not to propagate and cause problems. But those are just my two cents (about 2.8 dollar cents with current rates :p). Cheers, Tsjerk On Thu, Sep 1, 2011 at 2:41 PM, chris.neale at utoronto.ca wrote: I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not sure why PME would run fine and reaction field would give lincs warnings, but then again I have no experience with using a reaction field. Chris. On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that
Re: [gmx-users] reg g_rdf
vidhya sankar wrote: Dear justin, Thanks for your replies. i am doing Steered MD .. i would like to calculate radial Distribution function. of Moving group with respect to Fixed group . I am pulling only in Z direction then is it possible to calculate RDF along Z-direction. only . it means Is there is any option in g_rdf tools of gromacs Available? Not that I'm aware of, no. g_rdf works in three dimensions (default) or in the x-y plane (for membranes and interfacial systems). -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
[gmx-users] reg g_rdf
Dear justin, Thanks for you Immediate reply but When i surf the following site http://www.linux-support.com/cms/en/component/content/article/12-man-pages/31116-g-rdf-calculates-radial-distribution-functions-man1 I got he following information g_rdf calculates radial distribution functions in different ways. The normal method is around a (set of) particle(s), the other method is around the center of mass of a set of particles. With both methods rdf’s can also be calculated around axes parallel to the z-axis with option -xy it represents what? i need clarity 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] Gromacs versions 4.0.5 and 4.5.4
Dear Itamar, Thank you for your response. Why did you prefer to stick to 4.0.7? Is there something particularly difficult to transfer from 4.0.7 version to 4.5 version? Sapna On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass itamar.k...@monash.edu wrote: Hi Sapna, I had the same problem few weeks ago. Apparently, some parameters are different (eg. nstpcouple). Cheers, Itamar PS I found out that I prefer to stick to 4.0.7. On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote: Dear All, I have a simulation set up for a mixture of carbon dioxide and water system which runs perfectly on Gromacs 4.0.5 version. I have run these simulations at different temperatures and pressures, from the same starting configuration and the simulation proceeds smoothly in the 4.0.5 version. However, when I use exactly the same files to run the simulation in 4.5.4 version, the system crashes and writes out several pdb files. I was wondering if there is anything specific that has been changed between the two versions. I have pasted the mdp file of the simulations below. Any input will be much appreciated. MDP File title = 100% occupancy CO2 hydrate ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step nsteps = 1500 ; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = ; write coords nstvout = ; write velocities nstlog = 25000; print to logfile nstenergy = 500 ; print energies xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type= grid ; pairlist method coulombtype= PME rvdw = 1.2 ; cut-off for vdw rcoulomb = 1.2 ; cut-off for coulomb rlist= 1.2 ; cut-off for coulomb DispCorr = EnerPres Tcoupl = Nose-Hoover ref_t = 270 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic; pressure geometry tau_p= 1.0 1.0; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 30.5 30.5 ; ref pressure gen_vel = yes ; generate initial vel gen_temp = 260 ; initial temperature gen_seed = 372340 ; random seed constraint_algorithm = shake constraints = all-bonds --- Thank you, Sincerely, Sapna -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] reg g_rdf
vidhya sankar wrote: Dear justin, Thanks for you Immediate reply but When i surf the following site http://www.linux-support.com/cms/en/component/content/article/12-man-pages/31116-g-rdf-calculates-radial-distribution-functions-man1 I got he following information g_rdf calculates radial distribution functions in different ways. The normal method is around a (set of) particle(s), the other method is around the center of mass of a set of particles. With both methods rdf’s can also be calculated around axes parallel to the z-axis with option -xy it represents what? i need clarity I explained this previously. With the -xy option, only the x- and y-dimensions are considered relative to the reference, which makes sense for systems like proteins in membranes. -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] Gromacs versions 4.0.5 and 4.5.4
Hi Sapna, It is a good question, but such of personal preferences. I found out that my simulations tend to crash more often when I am using 4.5.5. It might be the General-reaction -field I use or something else, I am not sure. Also, it seems I will not gain much from upgrading, so I stick to 4.0.7. All this is not to say that 4.5.5 is not a good simulation package. It is a good and useful MD package, and I highly appreciate all the time and effort put into it. Best, Itamat PS, there are still people around using 3.3.3 or even 3.2.1, so I am not that behind. On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote: Dear Itamar, Thank you for your response. Why did you prefer to stick to 4.0.7? Is there something particularly difficult to transfer from 4.0.7 version to 4.5 version? Sapna On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass itamar.k...@monash.edu wrote: Hi Sapna, I had the same problem few weeks ago. Apparently, some parameters are different (eg. nstpcouple). Cheers, Itamar PS I found out that I prefer to stick to 4.0.7. On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote: Dear All, I have a simulation set up for a mixture of carbon dioxide and water system which runs perfectly on Gromacs 4.0.5 version. I have run these simulations at different temperatures and pressures, from the same starting configuration and the simulation proceeds smoothly in the 4.0.5 version. However, when I use exactly the same files to run the simulation in 4.5.4 version, the system crashes and writes out several pdb files. I was wondering if there is anything specific that has been changed between the two versions. I have pasted the mdp file of the simulations below. Any input will be much appreciated. MDP File title = 100% occupancy CO2 hydrate ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step nsteps = 1500 ; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = ; write coords nstvout = ; write velocities nstlog = 25000; print to logfile nstenergy = 500 ; print energies xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type= grid ; pairlist method coulombtype= PME rvdw = 1.2 ; cut-off for vdw rcoulomb = 1.2 ; cut-off for coulomb rlist= 1.2 ; cut-off for coulomb DispCorr = EnerPres Tcoupl = Nose-Hoover ref_t = 270 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic; pressure geometry tau_p= 1.0 1.0; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 30.5 30.5 ; ref pressure gen_vel = yes ; generate initial vel gen_temp = 260 ; initial temperature gen_seed = 372340 ; random seed constraint_algorithm = shake constraints = all-bonds --- Thank you, Sincerely, Sapna -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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
Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4
Itamar Kass wrote: Hi Sapna, It is a good question, but such of personal preferences. I found out that my simulations tend to crash more often when I am using 4.5.5. It might be the General-reaction -field I use or something else, I am not sure. Also, it seems I will not gain much from upgrading, so I stick to 4.0.7. The general instabilities result from tweaks to the handling of temperature and pressure coupling. Simply setting nsttcouple and nstpcouple to 1 during the initial equilibration seems to give stable systems. I'd say there are many reasons for upgrading. Tons of new features, bug fixes, etc. But then too, that's my personal preference ;) -Justin All this is not to say that 4.5.5 is not a good simulation package. It is a good and useful MD package, and I highly appreciate all the time and effort put into it. Best, Itamat PS, there are still people around using 3.3.3 or even 3.2.1, so I am not that behind. On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote: Dear Itamar, Thank you for your response. Why did you prefer to stick to 4.0.7? Is there something particularly difficult to transfer from 4.0.7 version to 4.5 version? Sapna On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass itamar.k...@monash.edu mailto:itamar.k...@monash.edu wrote: Hi Sapna, I had the same problem few weeks ago. Apparently, some parameters are different (eg. nstpcouple). Cheers, Itamar PS I found out that I prefer to stick to 4.0.7. On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote: Dear All, I have a simulation set up for a mixture of carbon dioxide and water system which runs perfectly on Gromacs 4.0.5 version. I have run these simulations at different temperatures and pressures, from the same starting configuration and the simulation proceeds smoothly in the 4.0.5 version. However, when I use exactly the same files to run the simulation in 4.5.4 version, the system crashes and writes out several pdb files. I was wondering if there is anything specific that has been changed between the two versions. I have pasted the mdp file of the simulations below. Any input will be much appreciated. MDP File title = 100% occupancy CO2 hydrate ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step nsteps = 1500 ; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = ; write coords nstvout = ; write velocities nstlog = 25000; print to logfile nstenergy = 500 ; print energies xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type= grid ; pairlist method coulombtype= PME rvdw = 1.2 ; cut-off for vdw rcoulomb = 1.2 ; cut-off for coulomb rlist= 1.2 ; cut-off for coulomb DispCorr = EnerPres Tcoupl = Nose-Hoover ref_t = 270 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic; pressure geometry tau_p= 1.0 1.0; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 30.5 30.5 ; ref pressure gen_vel = yes ; generate initial vel gen_temp = 260 ; initial temperature gen_seed = 372340 ; random seed constraint_algorithm = shake constraints = all-bonds --- Thank you, Sincerely, Sapna -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus
[gmx-users] Using CHARMM force fields in Gromacs
Dear all, I would like to do MD simulations of polymer binding to lipid bilayers. To that end I have generated the following components: - CgenFF-based force field for the polymers' monomeric units (tested in NAMD/CHARMM) - CHARMM36 lipid force field for the lipid bilayers with some added lipids (tested in NAMD/CHARMM) On the internet (http://www.gromacs.org/Downloads/User_contributions/Force_fields) I found the appropriate force fields (CgenFF and CHARMM36 for lipids). How do I combine those with the monomeric residues I have generated with ParamChem? I'm very familiar with Charmm, where all the necessary force field can be easily combined, but I have no idea how to do it Gromacs. Also worth mentioning: I will generate the initial structures of the lipid bilayers and of the polymers in Charmm for Charmm is the only package that can generate structures using just the internal coordinates in the force field. Thanks in advance for any help and tips, Jernej Zidar -- 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] calculation time
On 19/10/2011 5:26 AM, ahmet yıldırım wrote: Dear users, Sometimes, in the end ( in production simulation), Gromacs doesn't show calculation/finish time on screen, why? How can we show it? I don't know what you mean. 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
RE: [gmx-users] calculation time
You can get them in the log file. (At the bottom) Cheers, = Emanuel Birru PhD Candidate Faculty of Pharmacy and Pharmaceutical Sciences Monash University (Parkville Campus) 381 Royal Parade, Parkville Victoria 3052, Australia Tel: Int + 61 3 9903 9187 E-mail: emanuel.bi...@monash.edu www.pharm.monash.edu.au -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Wednesday, 19 October 2011 3:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] calculation time On 19/10/2011 5:26 AM, ahmet yıldırım wrote: Dear users, Sometimes, in the end ( in production simulation), Gromacs doesn't show calculation/finish time on screen, why? How can we show it? I don't know what you mean. 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 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] atom names in ffbonded.itp (oplsaa.ff)
Dear gmx-users, Does anyone know where can I find any explanations about the atom names in ffbonded.itp file in oplsaa.ff? I am trying to compare the amino acids' parameters in gromacs 4.5.4 with in tinker. Or where to find the default parameters gromacs takes for amino acids in its aminoacids.rtp file? For example, it is hard to guess what are C*, C_2 and C= in ffbonded.itp file: C*HC 10.10800 284512.0 ; C C3 10.15220 265265.6 ; END C_2 C3 10.15220 265265.6 ; END ... C= C= HC 1 120.000292.880 ; wlj C C= HC 1 119.700292.880 ; Thanks! jia -- 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] atom names in ffbonded.itp (oplsaa.ff)
On 19/10/2011 3:50 PM, mu xiaojia wrote: Dear gmx-users, Does anyone know where can I find any explanations about the atom names in ffbonded.itp file in oplsaa.ff? I am trying to compare the amino acids' parameters in gromacs 4.5.4 with in tinker. Or where to find the default parameters gromacs takes for amino acids in its aminoacids.rtp file? For example, it is hard to guess what are C*, C_2 and C= in ffbonded.itp file: C*HC 10.10800 284512.0 ; C C3 10.15220 265265.6 ; END C_2 C3 10.15220 265265.6 ; END ... C= C= HC 1 120.000292.880 ; wlj C C= HC 1 119.700292.880 ; Thanks! You need to cross-reference the OPLS atom types (full description in their literature, partial description in atomtypes.atp) with the atom names in ffnonbonded.itp to make ffbonded.itp more clear. 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
