Re: [gmx-users] a question about ensemble
On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo best Albert -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] a question about ensemble
Hello Flo: thank you so much for your kind comments. Yes, I would like to couple the pressure, it really helps a lot. best Albert On 05/03/2012 10:40 AM, Dommert Florian wrote: On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo best Albert -- 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] a question about ensemble
Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, I remark that Langevin method is used also for explicit water system! which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo Anyway, I think that there is no strict coupling between temperature and pressure coupling: You need to keep the tempaerature fixed around a value and the same for pressure, so I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is, in priciple, right. Maybe convergence speed changes, but in this case banchmark are quite useful very welcolme! best, Francesco best Albert -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] a question about ensemble
On Thu, 2012-05-03 at 10:45 +0200, Albert wrote: Hello Flo: thank you so much for your kind comments. Yes, I would like to couple the pressure, it really helps a lot. best Albert You're welcome. There is just one little typo On 05/03/2012 10:40 AM, Dommert Florian wrote: On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin it means thermostats and not barostats /Flo provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo best Albert -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] a question about ensemble
On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. /Flo which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo Anyway, I think that there is no strict coupling between temperature and pressure coupling: You need to keep the tempaerature fixed around a value and the same for pressure, so I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is, in priciple, right. Maybe convergence speed changes, but in this case banchmark are quite useful very welcolme! best, Francesco best Albert -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- 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
Re: [gmx-users] a question about ensemble
2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. Implicit Implicit solvent means accounting for the solvent presence without including water atoms, look at http://en.wikipedia.org/wiki/Implicit_solvation for details. Regarding the collision source, it is water! The gamma value represent the average collision frequence experienced by a protein atoms against water in solution. You have no water, so it models the water presence. In implicit water simulation, usually a value close to 50 ps-1 (the experimental values) is used, while for explicit water is used a value around 2-5ps-1 bacause water is present so it actually collides with protein. /Flo which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo Anyway, I think that there is no strict coupling between temperature and pressure coupling: You need to keep the tempaerature fixed around a value and the same for pressure, so I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is, in priciple, right. Maybe convergence speed changes, but in this case banchmark are quite useful very welcolme! best, Francesco best Albert -- 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 -- Florian Dommert Dipl. - Phys. Institute for
Re: [gmx-users] How to remove H atom from residue in gro file?
Ho THANKS MANY THANKS I'm sorry, I'm new to Gromacs, and finally got it. Thank you very much. Hagit. 2012/5/2 Mark Abraham mark.abra...@anu.edu.au On 2/05/2012 8:55 PM, Hagit G wrote: Hi gmx users, Well, I saw this question but the answer was not understood. I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a disulfide bond. Gromacs automatically adds H atoms. Although the disulfide bond is there, Gromacs ignore it because *each cystein is on a different chain*. So it adds H and therefor the disulfide bond is ruined during energy minimization. Is there any way to recreate such a disulfide bond (Please don't tell me again about -ss it works only on one chain. Moreover, the bond is existed on the pdf file.) or never ruined it at the first place? Yes, and the clue to how to combine the chains to give the mechanism a chance of working is on the page I linked last time: http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds 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] Incorrect number of parameters
Dear Gmx Users, I run the simulation of protein-ligand complex. Then I extracted coordinates for SMD - I want to pull away my ligand. I used to topology from pevious simulation, so I removed water, ions from topol.top as the size box will be changed etc. I placed protein-ligan in new box and solvated the system. Now I want to proceed to add ions: grompp -f minim.mdp -c Solv1.gro -p topol1.top -o ions1.tpr Fatal error: Incorrect number of parameters - found 3, expected 2 or 4 for LJ-14. Well there is nothing wrong with the topology files as I took them from previus simulation just removing water and ions. I think that Gromacs does not read whole file... Have you ever had such problem? I will appreciate any help, 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] a question about ensemble
On Thu, 2012-05-03 at 11:31 +0200, francesco oteri wrote: 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. Implicit Implicit solvent means accounting for the solvent presence without including water atoms, look at http://en.wikipedia.org/wiki/Implicit_solvation for details. Regarding the collision source, it is water! The gamma value represent And why do I simulate explicit water, if I have already included water in the collision term ? My question arose because you have written, that Langevin is also applied in explicit water simulations. Now you are only talking about implicit solvent simulations. For this purpose Langevin is surely fine, because it has especially develop for such a situation. /Flo the average collision frequence experienced by a protein atoms against water in solution. You have no water, so it models the water presence. In implicit water simulation, usually a value close to 50 ps-1 (the experimental values) is used, while for explicit water is used a value around 2-5ps-1 bacause water is present so it actually collides with protein. /Flo which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good
[gmx-users] Re: Re: Re: g_wham problem with negative COM differences
Thank you. I will use position geometry. I will actually need to rerun whole thing with slightly different peptide, so at the end I will not need those curves with recreated tpr-files. But at least I will now get pull code right from beginning and I got bit more understanding on pull code issues. -Anni -- Anni Kauko, Ph.D. Post Doctoral Researcher Structural Bioinformatics Laboratory Dept. of Biosciences, Biochemistry Åbo Akademi University 20520 Turku, Finland phone: +358 (0)2 215 4006 mobile: +358 (0)50-576 8656 -- 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] Proper 1-octanol box preparation
Hi GMX users! I prepared a box of 125 1-octanol molecules using genconf -f octanol_single_molecule.gro -nbox 5 5 5 and I tried to equilibrate this system in NPT ensemble to get proper density and nice cube box, similar to octanol configuration that one can download from http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies. But I always got something completely different. Some cluster of the molecules at the bottom of the simulation box, far away from dense cube configuration. You can see picture here: https://picasaweb.google.com/okroutil/Science#5738216101659210130. I tried different thermo- and barostats, different coupling times, compressibility, first NVT then NPT equil., but with no success. I also tried more chaotic initial configuration generated with genbox -ci ...gro - nmol 125 -box 5 5 5, no success. So my question is: is there some simulation protocol or some setting (higher pressure at the beginning of equilibration?), any trick suitable for this type of solvent? Till now I worked only with water and surfaces, so this is new area for me... Thank you very much for any answer and have a nice day! Ondrej Kroutil (Faculty of Health and Social Studies, South Bohemian University, Czech Republic) P.S.: I used gaff ff and topologies downloaded from http://virtualchemistry.org/molecules/111-87-5/index.php and this NPT eq. input: integrator = md dt = 0.002 nsteps = 50 comm_mode= linear nstcomm = 1000 nstxout = 0 nstxtcout= 100 nstvout = 0 nstfout = 0 nstlog = 500 nstlist = 10 ns_type = grid rlist= 1.4 coulombtype = PME rcoulomb = 1.4 rvdw = 1.4 constraints = none constraint_algorithm = lincs ;shake_tol = 0.1 lincs_iter = 1 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d optimize_fft= yes ; Nose-Hoover temperature coupling Tcoupl = berendsen tau_t = 1 tc_grps= system ref_t = 298. ; No Pressure Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.6e-5 ref_p = 1.0 ; OTHER periodic_molecules = no pbc = xyz gen_vel = yes gen_temp= 298.15 gen_seed= -1-- Ondřej Kroutil ,, Faculty of Health and Social Studies ))' University of South Bohemia OOO Jirovcova 24, Ceske Budejovice OOO The Czech Republic | OO E-mail: okrou...@gmail.com -- O Mobile: +420 736 537 190 -- 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] membrane simulation
Hi all, I'm new in Membrane simulations with Gromacs. I have to simulate a system made up of a protein just leant on a membrane patch which has previously been extended and made it free of periodicity (with trjconv). I'm reading the KALP15 in DPPCI Tutorial and, so far, I managed to obtain my protein (in pdb code) very close to the membrane surface by using editconf and cat command. At this point, I don't know how to get on. 1)How should I generate the topology file which includes the coordinates both of the protein and of the membrane? 2)Furthermore, the lipid molecules are listed in my pdb file with the abbreviation DPP, whereas I see that those ones are called DPPC in the Tutorial. Therefore, Should I replace DPP abbreviation with DPPC in my pdb file? Could this difference cause any bugs in the next steps? Any suggestion would be appreciated, Silvia -- 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] membrane simulation
On Thu, May 3, 2012 at 4:38 PM, scapr...@uniroma3.it wrote: Hi all, I'm new in Membrane simulations with Gromacs. I have to simulate a system made up of a protein just leant on a membrane patch which has previously been extended and made it free of periodicity (with trjconv). I'm reading the KALP15 in DPPCI Tutorial and, so far, I managed to obtain my protein (in pdb code) very close to the membrane surface by using editconf and cat command. At this point, I don't know how to get on. 1)How should I generate the topology file which includes the coordinates both of the protein and of the membrane? If you are using the ff53a6 FF then you need to add the appropriate lipid parameters in the ffnonbonded.itp and ffbonded.itp files (of ff53a6 FF) files which is very well explained in the tutorial. Then in your .top file you need to include the DPPC.itp. However, if you are using CHARMM36 FF, then you can directly use pdb2gmx on your system (I suppose DPPC is already included in it). If you wish to use the ff43a1 FF, then you can find the modified .itp files at https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial . 2)Furthermore, the lipid molecules are listed in my pdb file with the abbreviation DPP, whereas I see that those ones are called DPPC in the Tutorial. Therefore, Should I replace DPP abbreviation with DPPC in my pdb file? Could this difference cause any bugs in the next steps? PDB files use three letter convention for residue names. I think you can change them without any issue in the .gro file. -Anirban Any suggestion would be appreciated, Silvia -- 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] jointly-couple lipids to theromstat - MARTINI force-field
Hello, I am a bit confused by a comment which I find in all MARTINI example md.mdp scripts concerning the tc-groups : It is stated there to couple groups separately: MARTINI -Normal temperature and pressure coupling schemes can be used. It ; is recommended to couple individual groups in your system seperately I am simulating a mixed dppc:dppg membrane (see below my parameters). Even these two different lipids-types should be coupled separately? (and how about Na+ (Qd particles) and water - also separately?) I would greatly appreciate any comment on this issue. Thanks a lot Markus my parameter: ; Temperature coupling: tcoupl = berendsen ; Groups to couple separately: tc-grps = DPPC DPPG W NAA Protein -- 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] jointly-couple lipids to theromstat - MARTINI force-field
On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H. m.h.weinga...@uu.nl wrote: Hello, I am a bit confused by a comment which I find in all MARTINI example md.mdp scripts concerning the tc-groups : It is stated there to couple groups separately: MARTINI -Normal temperature and pressure coupling schemes can be used. It ; is recommended to couple individual groups in your system seperately I am simulating a mixed dppc:dppg membrane (see below my parameters). Even these two different lipids-types should be coupled separately? (and how about Na+ (Qd particles) and water - also separately?) I would greatly appreciate any comment on this issue. Thanks a lot Markus my parameter: ; Temperature coupling: tcoupl = berendsen ; Groups to couple separately: tc-grps = DPPC DPPG W NAA Protein Generally in membrane protein simulations different coupling groups are used to increase the accuracy of the calculations (more realistic). In your system you can make make three groups: Protein, Lipids(DPPC+DPPG) and Sol+Ions(Na+Qd) -Anirban -- 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
AW: [gmx-users] membrane simulation
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von Anirban Ghosh Gesendet: Donnerstag, 3. Mai 2012 13:39 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] membrane simulation On Thu, May 3, 2012 at 4:38 PM, scapr...@uniroma3.itmailto:scapr...@uniroma3.it wrote: Hi all, I'm new in Membrane simulations with Gromacs. I have to simulate a system made up of a protein just leant on a membrane patch which has previously been extended and made it free of periodicity (with trjconv). I'm reading the KALP15 in DPPCI Tutorial and, so far, I managed to obtain my protein (in pdb code) very close to the membrane surface by using editconf and cat command. At this point, I don't know how to get on. 1)How should I generate the topology file which includes the coordinates both of the protein and of the membrane? If you are using the ff53a6 FF then you need to add the appropriate lipid parameters in the ffnonbonded.itp and ffbonded.itp files (of ff53a6 FF) files which is very well explained in the tutorial. Then in your .top file you need to include the DPPC.itp. However, if you are using CHARMM36 FF, then you can directly use pdb2gmx on your system (I suppose DPPC is already included in it). If you wish to use the ff43a1 FF, then you can find the modified .itp files at https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial . 2)Furthermore, the lipid molecules are listed in my pdb file with the abbreviation DPP, whereas I see that those ones are called DPPC in the Tutorial. Therefore, Should I replace DPP abbreviation with DPPC in my pdb file? Could this difference cause any bugs in the next steps? PDB files use three letter convention for residue names. I think you can change them without any issue in the .gro file. -Anirban You can also simply replace DPP by DPPC in the pdb. But be careful that there is no shifting of the columns after the residue name, i.e. it should *NOT*look like this ATOM 1 C1 DPP 1 17.610 52.750 30.500 1.00 0.00 ATOM 2 C2 DPPC 1 16.160 50.940 30.040 1.00 0.00 ATOM 3 C3 DPPC 1 18.640 50.520 29.970 1.00 0.00 ATOM 4 N4 DPP 1 17.520 51.490 29.680 1.00 0.00 Any suggestion would be appreciated, Silvia -- gmx-users mailing listgmx-users@gromacs.orgmailto: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.orgmailto: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] Re: Proper 1-octanol box preparation
Hi, relating to the picture see: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions It's just a matter of periodic boundary conditions, you don't have two, but just one cluster of octanol. What i don't understand is, that your box doesn't collapse (becoming smaller) if you perfom the NPT simulation. Only thing is that i would search the value of compressibility of octanol, but this couldn't be the origin of the problem. Greetings Thomas Am 03.05.2012 12:23, schrieb gmx-users-requ...@gromacs.org: Hi GMX users! I prepared a box of 125 1-octanol molecules using genconf -f octanol_single_molecule.gro -nbox 5 5 5 and I tried to equilibrate this system in NPT ensemble to get proper density and nice cube box, similar to octanol configuration that one can download from http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies. But I always got something completely different. Some cluster of the molecules at the bottom of the simulation box, far away from dense cube configuration. You can see picture here: https://picasaweb.google.com/okroutil/Science#5738216101659210130. I tried different thermo- and barostats, different coupling times, compressibility, first NVT then NPT equil., but with no success. I also tried more chaotic initial configuration generated with genbox -ci ...gro - nmol 125 -box 5 5 5, no success. So my question is: is there some simulation protocol or some setting (higher pressure at the beginning of equilibration?), any trick suitable for this type of solvent? Till now I worked only with water and surfaces, so this is new area for me... Thank you very much for any answer and have a nice day! Ondrej Kroutil (Faculty of Health and Social Studies, South Bohemian University, Czech Republic) P.S.: I used gaff ff and topologies downloaded from http://virtualchemistry.org/molecules/111-87-5/index.php and this NPT eq. input: integrator = md dt = 0.002 nsteps = 50 comm_mode= linear nstcomm = 1000 nstxout = 0 nstxtcout= 100 nstvout = 0 nstfout = 0 nstlog = 500 nstlist = 10 ns_type = grid rlist= 1.4 coulombtype = PME rcoulomb = 1.4 rvdw = 1.4 constraints = none constraint_algorithm = lincs ;shake_tol = 0.1 lincs_iter = 1 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d optimize_fft= yes ; Nose-Hoover temperature coupling Tcoupl = berendsen tau_t = 1 tc_grps= system ref_t = 298. ; No Pressure Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.6e-5 ref_p = 1.0 ; OTHER periodic_molecules = no pbc = xyz gen_vel = yes gen_temp= 298.15 gen_seed= -1-- Ond??ej Kroutil -- 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] jointly-couple lipids to theromstat - MARTINI force-field
The separation of groups for temperature control is originally necessary to avoid (or correct for) temperature gradient in the system, which occurs when systems parts have different frequencies of motions. Typically the water molecules and a protein would be separated to avoid the freezing of the protein and the heating up of the solvent. It would not make much difference to couple the dppc and dppg lipid groups separately or together. To form a separate group you need a sufficient amount of particle to avoid large (and therefore more difficult to control) fluctuations. Ions are generally coupled to the solvent they are embedded into. Anirban suggestion is fine. On May 3, 2012, at 1:56 PM, Anirban Ghosh wrote: On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H. m.h.weinga...@uu.nl wrote: Hello, I am a bit confused by a comment which I find in all MARTINI example md.mdp scripts concerning the tc-groups : It is stated there to couple groups separately: MARTINI -Normal temperature and pressure coupling schemes can be used. It ; is recommended to couple individual groups in your system seperately I am simulating a mixed dppc:dppg membrane (see below my parameters). Even these two different lipids-types should be coupled separately? (and how about Na+ (Qd particles) and water - also separately?) I would greatly appreciate any comment on this issue. Thanks a lot Markus my parameter: ; Temperature coupling: tcoupl = berendsen ; Groups to couple separately: tc-grps = DPPC DPPG W NAA Protein Generally in membrane protein simulations different coupling groups are used to increase the accuracy of the calculations (more realistic). In your system you can make make three groups: Protein, Lipids(DPPC+DPPG) and Sol+Ions(Na+Qd) -Anirban -- 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 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] CHARMM36 and Dispersion correction
Hi ALL, I am simulating a membrane protein immersed in a POPC bilayer using CHARMM36 FF in GROMACS 4.5.5. In NVT and NPT (i.e. in equilibration and production runs) should I use the dispersion correction or not (as suggested in some previous posts)? And if NOT using dispersion correction, then should I use vdwtype as switch? Any suggestion is welcome. Regards, Anirban -- 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] missing gbsa parameters
hi guys, i'm trying to simulate some receptor ligand system with implicit solvent using gbsa in order to get a quick folding of some tens of N-terminal peptides. this works pretty well with the target only applying the amber99sb FF. as soon as i try to simulate it together with the ligand which was parameterized with acpype (using amber-antechamber), i get the following error at the grompp step: GB parameter(s) missing or negative for atom type 'cc' GB parameter(s) missing or negative for atom type 'n' ... Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 15 atomtypes or they might be negative. the atom types in the error output are exactly those listed in the [ atom types ] section of the ligand's topology file created with acpype/antechamber. however, the atom types mentioned here ARE listed in the respective gbsa.itp file which looks like this: [ implicit_genborn_params ] ; atype sar st pi gbr hct ... CC 0.1721 1.5540.18750.72 ; C does anybody know how to handle this problem? and is there someone that can tell me how (with which parameter values) to add GAFF atom types like e.g. ss, hn, hx, os to the gbsa.itp file? thanks in advance and take care 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
Re: [gmx-users] missing gbsa parameters
On 5/3/12 9:34 AM, Vedat Durmaz wrote: hi guys, i'm trying to simulate some receptor ligand system with implicit solvent using gbsa in order to get a quick folding of some tens of N-terminal peptides. this works pretty well with the target only applying the amber99sb FF. as soon as i try to simulate it together with the ligand which was parameterized with acpype (using amber-antechamber), i get the following error at the grompp step: GB parameter(s) missing or negative for atom type 'cc' GB parameter(s) missing or negative for atom type 'n' ... Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 15 atomtypes or they might be negative. the atom types in the error output are exactly those listed in the [ atom types ] section of the ligand's topology file created with acpype/antechamber. however, the atom types mentioned here ARE listed in the respective gbsa.itp file which looks like this: [ implicit_genborn_params ] ; atype sar st pi gbr hct ... CC 0.172 1 1.554 0.1875 0.72 ; C Atom types are case-sensitive, thus cc and CC are not, in fact, the same. does anybody know how to handle this problem? and is there someone that can tell me how (with which parameter values) to add GAFF atom types like e.g. ss, hn, hx, os to the gbsa.itp file? You can probably assign the atom types you need based on chemical similarity to existing atom types/functional groups. -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] membrane simulation
Than you very much for your reply. I'm using ffnonbonded.itp etc. I still have some doubts regarding to the topology file which has to be used. Should I work and modify the topology file associated with the protein by adding the information related to the DPPC lipids as reported in the manual? I mean: is it ok if I use the topology file created at the beginning from pdb2gmx command on the protein and modify it? thanks. -- 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] membrane simulation
On 5/3/12 10:39 AM, scapr...@uniroma3.it wrote: Than you very much for your reply. I'm using ffnonbonded.itp etc. I still have some doubts regarding to the topology file which has to be used. Should I work and modify the topology file associated with the protein by adding the information related to the DPPC lipids as reported in the manual? I mean: is it ok if I use the topology file created at the beginning from pdb2gmx command on the protein and modify it? That is an appropriate workflow. The tutorial walks you through all the necessary steps, so do follow it carefully. -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] Lamb-Protein
On 5/3/12 10:52 AM, francesco oteri wrote: Dear gromacs users, I am using g_energy to extract energies and I noticed that, amon the different groups, there groups like Lamb-Protein,Lamb-Water_and_ions and other names I dont know. I am wondering whether exist a guide explaining the differet contribution displayed by g_energy; Most are fairly obvious, others are discussed on gromacs.org. In the case of Lamb- terms, these are the lambda values when the free energy code is being utilized. -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] Lamb-Protein
Hi Justin, I have free-energy = no in my .mdp file, but I still see this value in g_energy. It should be absent or always 1 while the values by g_energy are close to 1 but still fluctuating along the trajectory. So, can you explain me how the value is used by gromacs? Francesco 2012/5/3 Justin A. Lemkul jalem...@vt.edu On 5/3/12 10:52 AM, francesco oteri wrote: Dear gromacs users, I am using g_energy to extract energies and I noticed that, amon the different groups, there groups like Lamb-Protein,Lamb-Water_and_**ions and other names I dont know. I am wondering whether exist a guide explaining the differet contribution displayed by g_energy; Most are fairly obvious, others are discussed on gromacs.org. In the case of Lamb- terms, these are the lambda values when the free energy code is being utilized. -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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] how to extract trajectories into individual pdb file?
hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. thank you very much best Albert -- 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] how to extract trajectories into individual pdb file?
On 4/05/2012 1:10 AM, Albert wrote: hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. See trjconv -h 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] how to extract trajectories into individual pdb file?
In particular, look at the option -sep 2012/5/3 Mark Abraham mark.abra...@anu.edu.au On 4/05/2012 1:10 AM, Albert wrote: hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. See trjconv -h 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] how to extract trajectories into individual pdb file?
On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- 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] how to extract trajectories into individual pdb file?
-fit 2012/5/3 Albert mailmd2...@gmail.com On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] Lamb-Protein
On 5/3/12 11:04 AM, francesco oteri wrote: Hi Justin, I have free-energy = no in my .mdp file, but I still see this value in g_energy. It should be absent or always 1 while the values by g_energy are close to 1 but still fluctuating along the trajectory. So, can you explain me how the value is used by gromacs? Sorry, what I said before was wrong. I mistook the energy term. It's actually related to temperature coupling and shows up when using Berendsen or V-rescale. The actual term is defined in the original 1984 Berendsen coupling paper (eq 10 and 11). -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] how to extract trajectories into individual pdb file?
thank you very much. I found a problem : there is no option to select step. eg: I would like to export one snapshot at each 10ps, I don't find such kind of options.. THX On 05/03/2012 05:21 PM, francesco oteri wrote: -fit 2012/5/3 Albert mailmd2...@gmail.com mailto:mailmd2...@gmail.com On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- gmx-users mailing list gmx-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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] how to extract trajectories into individual pdb file?
On 5/3/12 11:58 AM, Albert wrote: thank you very much. I found a problem : there is no option to select step. eg: I would like to export one snapshot at each 10ps, I don't find such kind of options.. That's what you can use -skip or -dt for. Alternatively, dump out frames at specific times with -dump. Note that you can find all of this, and more, in the help info printed by trjconv, as Mark originally suggested. -Justin THX On 05/03/2012 05:21 PM, francesco oteri wrote: -fit 2012/5/3 Albert mailmd2...@gmail.com mailto:mailmd2...@gmail.com On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- gmx-users mailing list gmx-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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] Error: 1 atoms are not part of any of the T-Coupling groups
Dear, I am working in complex protein which contains one ligand and one Mg2+ ion. I am got an error while running grompp for NVT. grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr --- Program grompp, VERSION 4.5.3 Source code file: readir.c, line: 1402 Ftal error: 1 atoms are not part of any of the T-Coupling groups -- For creating the index file before grompp i used the following command make_ndx -f em.gro -o index.ndx 0 System : 248986 atoms 1 Protein : 5019 atoms 2 Protein-H : 3975 atoms 3 C-alpha : 519 atoms 4 Backbone: 1557 atoms 5 MainChain : 2077 atoms 6 MainChain+Cb: 2556 atoms 7 MainChain+H : 2575 atoms 8 SideChain : 2444 atoms 9 SideChain-H : 1898 atoms 10 Prot-Masses : 5019 atoms 11 non-Protein : 243967 atoms 12 Other :24 atoms 13 MG2+: 1 atoms 14 UNK :23 atoms 15 NA : 1 atoms 16 Water : 243942 atoms 17 SOL : 243942 atoms 18 non-Water : 5044 atoms 19 Ion : 1 atoms 20 MG2+: 1 atoms 21 UNK :23 atoms 22 NA : 1 atoms 23 Water_and_ions : 243943 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 'ri': residue index 1 | 14 Copied index group 1 'Protein' Copied index group 14 'UNK' Merged two groups with OR: 5019 23 - 5042 24 Protein_UNK : 5042 atoms q nvt.mdp i used title = Protein-ligand complex NVT equilibration define = -DPOSRES integrator = md nsteps = 5 dt = 0.002 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 energygrps = Protein UNK continuation= no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 0.9 rcoulomb= 0.9 rvdw= 1.4 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = Protein_UNK Water_and_ions tau_t = 0.1 0.1 ref_t = 300 300 pcoupl = no pbc = xyz DispCorr= EnerPres ; Velocity generation gen_vel = yes gen_temp= 300 gen_seed= -1 I am not clear how i can add MG2+ while creating index.ndx file. Please help me out. P.Kalaiarasan National Centre of Applied Human Genetics School of Life Sciences JNU New Delhi India -- 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] Error: 1 atoms are not part of any of the T-Coupling groups
On 5/3/12 12:32 PM, kalai arasan wrote: Dear, I am working in complex protein which contains one ligand and one Mg2+ ion. I am got an error while running grompp for NVT. grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr --- Program grompp, VERSION 4.5.3 Source code file: readir.c, line: 1402 Ftal error: 1 atoms are not part of any of the T-Coupling groups -- For creating the index file before grompp i used the following command make_ndx -f em.gro -o index.ndx 0 System : 248986 atoms 1 Protein : 5019 atoms 2 Protein-H : 3975 atoms 3 C-alpha : 519 atoms 4 Backbone: 1557 atoms 5 MainChain : 2077 atoms 6 MainChain+Cb: 2556 atoms 7 MainChain+H : 2575 atoms 8 SideChain : 2444 atoms 9 SideChain-H : 1898 atoms 10 Prot-Masses : 5019 atoms 11 non-Protein : 243967 atoms 12 Other :24 atoms 13 MG2+: 1 atoms 14 UNK :23 atoms 15 NA : 1 atoms 16 Water : 243942 atoms 17 SOL : 243942 atoms 18 non-Water : 5044 atoms 19 Ion : 1 atoms 20 MG2+: 1 atoms 21 UNK :23 atoms 22 NA : 1 atoms 23 Water_and_ions : 243943 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char name: group 'case': case sensitive 'q': save and quit 'ri': residue index 1 | 14 Copied index group 1 'Protein' Copied index group 14 'UNK' Merged two groups with OR: 5019 23 - 5042 24 Protein_UNK : 5042 atoms q nvt.mdp i used title = Protein-ligand complex NVT equilibration define = -DPOSRES integrator = md nsteps = 5 dt = 0.002 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 energygrps = Protein UNK continuation= no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 0.9 rcoulomb= 0.9 rvdw= 1.4 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = Protein_UNK Water_and_ions tau_t = 0.1 0.1 ref_t = 300 300 pcoupl = no pbc = xyz DispCorr= EnerPres ; Velocity generation gen_vel = yes gen_temp= 300 gen_seed= -1 I am not clear how i can add MG2+ while creating index.ndx file. Please help me out. Three approaches: 1. Create a group that replaces Water_and_ions with one that contains the MG2+ ion within the solvent 2. Add MG2+ to residuetypes.dat so that it is recognized as an ion 3. Couple the MG2+ and protein/ligand together, as might make the most physical sense -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] a question about ensemble
Hi Florian, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. The use of Langevin dynamics (SD) to mimic solvant implicitely or as a thermostat in explicit systems depends on the friction coefficient you choose. It has to be chosen with care, see for example http://dx.doi.org/10.1007/b99427 or the GROMACS manual. In explicit simulations, SD with the appropriate choice of friction coefficient can be seen as a local thermostat. The advantage is that it samples the canonical ensemble (in the old versions of GROMACS it was the only way to get the canonical ensemble before the implementation of Nose-Hoover or velocity rescaling). Ciao, Patrick -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- 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] CHARMM36 and Dispersion correction
In the .mdp file in the collection I provided yesterday, DispCorr was turned off and vdwtype set to switch with a switching distance rvdw_switch = 0.8 I copied most of my mdp values from Oak Ridge National Laboratory Center for Molecular Biophysics Roland Schulz's gromacs cheatsheet: http://cmb.ornl.gov/members/z8g/cheat-sheet-for-gromacs On 2012-05-03 06:38:22PM +0530, Anirban Ghosh wrote: Hi ALL, I am simulating a membrane protein immersed in a POPC bilayer using CHARMM36 FF in GROMACS 4.5.5. In NVT and NPT (i.e. in equilibration and production runs) should I use the dispersion correction or not (as suggested in some previous posts)? And if NOT using dispersion correction, then should I use vdwtype as switch? Any suggestion is welcome. Regards, Anirban -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] trjconv correct the pbc before analysis
Thanks Justin and Mark, I compared g_rama's results for no pbc treated trajectory and pbc treated trajectory, it seems they are the same. So gromacs' analysis tools know how to deal with the broken molecules. But if one want to extract such coordinates out for computing it myself, it is necessary to -pbc mol first, otherwise the molecules might be broken for calculating scripts like matlab. good to know this, thanks! On Wed, May 2, 2012 at 8:03 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 03/05/12, *mu xiaojia *muxiaojia2...@gmail.com wrote: Dear gmx users, I have a question about using the trjconv -pbc options before analyzing my trajectory. It's stated by Justin's tutorial that: use trjconv to account for any periodicity in the system. The protein will diffuse through the unit cell, and may appear to jump across to the other side of the box. To account for such actions, issue the following: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html ) But for my system, I study the short peptides' aggregation, I have many short peptides(not one or two single proteins) and waters, when I use -pbc nojump to treat my trajectory, it only gives me correct short peptides(no across out of the box), but the water is quite diffused. (I guess it is different with the tutorial since on it the protein is 1 or 2 polymers) So (1)how should I analyze such results if I want to study both short peptides(correct coordinates, no crossings) and waters(diffused and crossed box)? That entirely depends on what you are trying to observe. You may find you need multiple representations of the trajectory for different purposes. (2) I tried all the pbc options(even try them one after another, like mol first, nojump second), currently no clues of how to get both peptides and waters correct at the same time. Command for correct protein but incorrect waters' coordinates is: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc nojump Thanks very much, I appreciate any suggestions. If molecules diffuse across the periodic boundaries, you cannot have a single representation that is both compact and lacks jumps. 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
Re: [gmx-users] NBFIX to gromacs
Dear Mr. Lai, I see. I'll look more deeply into it, thanks for your answer. Ricardo. De: Peter C. Lai p...@uab.edu Para: Ricardo O. S. Soares ross_...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Quarta-feira, 2 de Maio de 2012 20:35 Assunto: Re: [gmx-users] NBFIX to gromacs The problem is that functype 1 for [ pairtypes ] when gromacs uses a CHARMM forcefield is that gromacs treats them as 1-4 interactions. You will have to ask/wait for someone familiar with the gromacs source to say if there is a different functype available to use to override non-1-4 interactions with the given pair parameters that you want to specify. On 2012-05-02 12:35:17PM -0700, Ricardo O. S. Soares wrote: Dear Mr. Peter C. Lai, I appreciate your kind response. I apologize for the delay on my part. This NBFIX parameters that I'm working with came from the str file in http://terpconnect.umd.edu/~jbklauda/research/download/chol_new.str , which dates from 2012. I successfully converted this whole file, now I'm wondering about this NBFIX section. I'm thinking about converting these values from Kcal to KJ and Angstrom to nm, adapt and append to [ pairtypes ]. Could this be the right move? Thanks again, Ricardo. De: Peter C. Lai p...@uab.edu Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Segunda-feira, 30 de Abril de 2012 20:46 Assunto: Re: [gmx-users] NBFIX to gromacs NBFIXes haven't been used in charmm for a long time (1998), although current versions still read topologies containing those records. Perhaps you should reparameterize your molecule with a more current version? (Or start with the coordinate file and use pdb2gmx with the converted ff). The only thing I can think of if you really need to do it is to create new atom types. As far as I know, gromacs only supports 1 set of vdw coefficients and a 1-4 pair. On 2012-04-30 01:30:59PM -0700, Ricardo O. S. Soares wrote: Hello GMX users, does anyone that dealt with Charmm before knows how to translate the NBFIX section into a Gromacs ff format? After convertion from KCal to KJ, does it go into [pairtypes]? I see that it concerns to corrections in LJ interactions, however the charmm documentation seems a bit unclear to me. Thanks again, Ricardo. -- 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 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 -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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: Proper 1-octanol box preparation
Dear Ondrej - I would start with a high pressure simulation (say, P=100 bar) for 200-500 ps. After this run, the system will be compressed to its more realistic liquid density. Then, go back to P=1 bar and re-equilibrate for 100-200 ps. I guess, if the temperature were higher, the density would converge faster. What is the shear viscosity of octanol, something around 5-10 cP? Regards, Vitaly Chaban -- Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA I prepared a box of 125 1-octanol molecules using genconf -f octanol_single_molecule.gro -nbox 5 5 5 and I tried to equilibrate this system in NPT ensemble to get proper density and nice cube box, similar to octanol configuration that one can download from http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies. But I always got something completely different. Some cluster of the molecules at the bottom of the simulation box, far away from dense cube configuration. You can see picture here: https://picasaweb.google.com/okroutil/Science#5738216101659210130. I tried different thermo- and barostats, different coupling times, compressibility, first NVT then NPT equil., but with no success. I also tried more chaotic initial configuration generated with genbox -ci ...gro - nmol 125 -box 5 5 5, no success. So my question is: is there some simulation protocol or some setting (higher pressure at the beginning of equilibration?), any trick suitable for this type of solvent? Till now I worked only with water and surfaces, so this is new area for me... Thank you very much for any answer and have a nice day! Ondrej Kroutil (Faculty of Health and Social Studies, South Bohemian University, Czech Republic) P.S.: I used gaff ff and topologies downloaded from http://virtualchemistry.org/molecules/111-87-5/index.php and this NPT eq. input: integrator = md dt = 0.002 nsteps = 50 comm_mode = linear nstcomm = 1000 nstxout = 0 nstxtcout = 100 nstvout = 0 nstfout = 0 nstlog = 500 nstlist = 10 ns_type = grid rlist = 1.4 coulombtype = PME rcoulomb = 1.4 rvdw = 1.4 constraints = none constraint_algorithm = lincs ;shake_tol = 0.1 lincs_iter = 1 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d optimize_fft = yes ; Nose-Hoover temperature coupling Tcoupl = berendsen tau_t = 1 tc_grps = system ref_t = 298. ; No Pressure Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.6e-5 ref_p = 1.0 ; OTHER periodic_molecules = no pbc = xyz gen_vel = yes gen_temp = 298.15 gen_seed = -1-- Ondřej Kroutil -- 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] Proper 1-octanol box preparation
Did you plot the box volume, box dimensions or density with simulation time? Over those 500,000 steps it should be shrinking. It would also be a good idea if you made a box size and number of molecules that is at least close to the density of octanol. From the image you included, the box appears to be at least 3 times too large for the number of molecules you have inserted. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Ondrej Kroutil Sent: Thursday, 3 May 2012 8:23 PM To: gmx-users@gromacs.org Subject: [gmx-users] Proper 1-octanol box preparation Hi GMX users! I prepared a box of 125 1-octanol molecules using genconf -f octanol_single_molecule.gro -nbox 5 5 5 and I tried to equilibrate this system in NPT ensemble to get proper density and nice cube box, similar to octanol configuration that one can download from http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies . But I always got something completely different. Some cluster of the molecules at the bottom of the simulation box, far away from dense cube configuration. You can see picture here: https://picasaweb.google.com/okroutil/Science#5738216101659210130. I tried different thermo- and barostats, different coupling times, compressibility, first NVT then NPT equil., but with no success. I also tried more chaotic initial configuration generated with genbox -ci ...gro - nmol 125 -box 5 5 5, no success. So my question is: is there some simulation protocol or some setting (higher pressure at the beginning of equilibration?), any trick suitable for this type of solvent? Till now I worked only with water and surfaces, so this is new area for me... Thank you very much for any answer and have a nice day! Ondrej Kroutil (Faculty of Health and Social Studies, South Bohemian University, Czech Republic) P.S.: I used gaff ff and topologies downloaded from http://virtualchemistry.org/molecules/111-87-5/index.php and this NPT eq. input: integrator = md dt = 0.002 nsteps = 50 comm_mode= linear nstcomm = 1000 nstxout = 0 nstxtcout= 100 nstvout = 0 nstfout = 0 nstlog = 500 nstlist = 10 ns_type = grid rlist= 1.4 coulombtype = PME rcoulomb = 1.4 rvdw = 1.4 constraints = none constraint_algorithm = lincs ;shake_tol = 0.1 lincs_iter = 1 fourierspacing = 0.1 pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d optimize_fft= yes ; Nose-Hoover temperature coupling Tcoupl = berendsen tau_t = 1 tc_grps= system ref_t = 298. ; No Pressure Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.6e-5 ref_p = 1.0 ; OTHER periodic_molecules = no pbc = xyz gen_vel = yes gen_temp= 298.15 gen_seed= -1-- Ondřej Kroutil ,, Faculty of Health and Social Studies ))' University of South Bohemia OOO Jirovcova 24, Ceske Budejovice OOO The Czech Republic | OO E-mail: okrou...@gmail.com -- O Mobile: +420 736 537 190 -- 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] trjconv correct the pbc before analysis
On 4/05/2012 4:03 AM, mu xiaojia wrote: Thanks Justin and Mark, I compared g_rama's results for no pbc treated trajectory and pbc treated trajectory, it seems they are the same. So gromacs' analysis tools know how to deal with the broken molecules. Caveat: some tools seem to be better than others at dealing with PBC. There are known question marks hovering over g_dist, g_bond and g_mindist. This situation is probably a consequence of different tools being developed at different times during the evolution of the software suite. Mark But if one want to extract such coordinates out for computing it myself, it is necessary to -pbc mol first, otherwise the molecules might be broken for calculating scripts like matlab. good to know this, thanks! On Wed, May 2, 2012 at 8:03 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 03/05/12, *mu xiaojia *muxiaojia2...@gmail.com mailto:muxiaojia2...@gmail.com wrote: Dear gmx users, I have a question about using the trjconv -pbc options before analyzing my trajectory. It's stated by Justin's tutorial that: use trjconv to account for any periodicity in the system. The protein will diffuse through the unit cell, and may appear to jump across to the other side of the box. To account for such actions, issue the following: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html ) But for my system, I study the short peptides' aggregation, I have many short peptides(not one or two single proteins) and waters, when I use -pbc nojump to treat my trajectory, it only gives me correct short peptides(no across out of the box), but the water is quite diffused. (I guess it is different with the tutorial since on it the protein is 1 or 2 polymers) So (1)how should I analyze such results if I want to study both short peptides(correct coordinates, no crossings) and waters(diffused and crossed box)? That entirely depends on what you are trying to observe. You may find you need multiple representations of the trajectory for different purposes. (2) I tried all the pbc options(even try them one after another, like mol first, nojump second), currently no clues of how to get both peptides and waters correct at the same time. Command for correct protein but incorrect waters' coordinates is: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc nojump Thanks very much, I appreciate any suggestions. If molecules diffuse across the periodic boundaries, you cannot have a single representation that is both compact and lacks jumps. Mark -- gmx-users mailing list gmx-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 -- 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] Incorrect number of parameters
On 3/05/2012 8:08 PM, Steven Neumann wrote: Dear Gmx Users, I run the simulation of protein-ligand complex. Then I extracted coordinates for SMD - I want to pull away my ligand. I used to topology from pevious simulation, so I removed water, ions from topol.top as the size box will be changed etc. I placed protein-ligan in new box and solvated the system. Now I want to proceed to add ions: grompp -f minim.mdp -c Solv1.gro -p topol1.top -o ions1.tpr Fatal error: Incorrect number of parameters - found 3, expected 2 or 4 for LJ-14. Well there is nothing wrong with the topology files as I took them from previus simulation just removing water and ions. I think that Gromacs does not read whole file... Have you ever had such problem? The simplest possible explanation is that your modifications to the .top are not as simple as you believe they are. Check that the original .top works as expected, and use the diff tool to compare the original and modified versions. 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] any method to determine gaussian curvature of phase
Hi, I wanted to numerically determine the gaussian curvature of a phase obtained by self-assembly of surfactants. I was wondering whether any one can suggest any tool or any program which can create a 3D grid and then calculate the gaussian curvature on points on the 3D grid . Thanks Sanku-- 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
