[gmx-users] energy minimization
Hi every body in order to protein- ligand docking, energy minimization was done by GROMACS. I did the following steps for insulin pdb file: 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce 2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr 3-mdrun -v -deffnm em 4- editconf -f em.gro -o final.pdb -c -d 1.0 -bt cubic everything was perfect, but the final pdb file has two problems: 1- chain ID was missed. 2- insulin contains two chains (A B) which connect by disulfide bond, but after energy minimization, two chains are separated. I would like to know how to solve these problems? best regards -- *Marzieh Dehghan PhD Candidate of Biochemistry Institute of biochemistry and Biophysics (IBB) University of Tehran, Tehran- Iran.* -- 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] Funky output trajectory (lines all over the place)
I tried minimizing a box of cyclohexanes and water. The first frame is fine, but after that seemingly random lines form in vmd with the cyclohexanes. The waters seem to minimizing just fine though. I am sure I am just doing something extremely silly and I just don't know it because of ignorance. I have no formal training on simulations, you are my only hope! Perhaps using the em.gro with the em.trr is not the correct way to visualize? I used the command: vmd em.gro em.trr Or something is wrong with my em.mdp? em.mdp: http://pastebin.com/raw.php?i=LPPN5xRF Commands used: http://pastebin.com/raw.php?i=Jk0fKLJj Here are all the files, in case you need them: http://www.sendspace.com/file/gx8j97 Sorry for dumping all of this, but I am genuinely stuck. I've tried reading about the mdp file format but i only understand ~5%. If I could have done more I would have tried :/ Thank you all, it is really appreciated. -Jonathan Saboury -- 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: gmx-users Digest, Vol 113, Issue 101
That said, there is an spc.itp within the AMBER subdirectories that needs to be #included more explicitly, i.e. #include amber99sb.ff/spc.itp May I ask why you are using SPC? The AMBER force fields were parametrized with TIP3P, so I see no viable reason to use a different water model. Ah, fixed and works like a charm, thank you :) To be completely honest I was using it out of ignorance. I've just been checking what has worked for me in tutorials and been working from there to something I am more interested in. It's not a bug, because genbox does not advertise such a feature. genbox is hard-coded to only ever deal with water. Anything else is up to the user. Interesting, any reason a user would not want such a feature? Any force field can be parametrized to give correct target data, especially for a molecule as simple as cyclohexane. What I use is a complex question, because it depends entirely upon the task at hand :) Can you list a few so I can go check them out on my own? It would be appreciated :) Thank you Justin, I appreciate your time you give helping me :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Calculation of binding enthalpy in vacuum
Dear Gromacs users, I’m trying to calculate the binding enthalpy of a host molecule with a guest molecule in vacuum. I cannot perform QM calculations because some systems I’m studying are too large. I know that free energy calculations are possible with Gromacs, but they require some cautions. Instead of calculating free energies, I have subtracted the total energy of the guest (△EG) and the host (△EH) from the total energy of the complex (△EC). In other words, △E = △EC - △EH - △EG, where all energies are total energy obtained from g_energy. In this case, would the calculated △E be the binding enthalpy in vacuum (gas phase)? I’ve tried QM calculations, and the △E obtained with Gromacs matches QM calculations in ~ 5% range. But I’m still unsure on how proper this method is. Could you advise me on this? Thank you in advance, John Lee -- 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] script to convert the TIP3P water model into TIP4P
Hello all, It is not a gromacs problem per se, but I hope that some gromacs users can help me. I would to do simulations of phospholipid bilayers with the TIP4P/2005 water model. I have downloaded in the Klauda's website several bilayer starting conformations. However, since CHARMM uses the TIP3 water model, I am confused to convert the water coordinates into a water four sites. Does somebody has a little script to share with me that can help me? Thank you for kindly help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculation of binding enthalpy in vacuum
Dear John - I think you can achieve the goal even faster if you just define two groups, such as MOL1 and MOL2 in MDP and then see the interaction energy between them using g_energy. 5% is a decent agreement. Usually, even basis set superposition error is larger (if you include this correction). Dr. Vitaly V. Chaban On Mon, Sep 23, 2013 at 9:32 AM, Jong Wha Lee jongwh...@postech.ac.kr wrote: Dear Gromacs users, I’m trying to calculate the binding enthalpy of a host molecule with a guest molecule in vacuum. I cannot perform QM calculations because some systems I’m studying are too large. I know that free energy calculations are possible with Gromacs, but they require some cautions. Instead of calculating free energies, I have subtracted the total energy of the guest (△EG) and the host (△EH) from the total energy of the complex (△EC). In other words, △E = △EC - △EH - △EG, where all energies are total energy obtained from g_energy. In this case, would the calculated △E be the binding enthalpy in vacuum (gas phase)? I’ve tried QM calculations, and the △E obtained with Gromacs matches QM calculations in ~ 5% range. But I’m still unsure on how proper this method is. Could you advise me on this? Thank you in advance, John Lee -- 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] Funky output trajectory (lines all over the place)
Dear Jonathan - Is it not a PBC effect? Try to display atoms as spheres - it will look better. Otherwise, use the options in trjconv to remove PBC in the visualized structure(s). Dr. Vitaly V. Chaban On Mon, Sep 23, 2013 at 9:22 AM, Jonathan Saboury jsab...@gmail.com wrote: I tried minimizing a box of cyclohexanes and water. The first frame is fine, but after that seemingly random lines form in vmd with the cyclohexanes. The waters seem to minimizing just fine though. I am sure I am just doing something extremely silly and I just don't know it because of ignorance. I have no formal training on simulations, you are my only hope! Perhaps using the em.gro with the em.trr is not the correct way to visualize? I used the command: vmd em.gro em.trr Or something is wrong with my em.mdp? em.mdp: http://pastebin.com/raw.php?i=LPPN5xRF Commands used: http://pastebin.com/raw.php?i=Jk0fKLJj Here are all the files, in case you need them: http://www.sendspace.com/file/gx8j97 Sorry for dumping all of this, but I am genuinely stuck. I've tried reading about the mdp file format but i only understand ~5%. If I could have done more I would have tried :/ Thank you all, it is really appreciated. -Jonathan Saboury -- 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] script to convert the TIP3P water model into TIP4P
I am confused. Why do you want 4-sites water? Dr. Vitaly V. Chaban On Mon, Sep 23, 2013 at 10:36 AM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello all, It is not a gromacs problem per se, but I hope that some gromacs users can help me. I would to do simulations of phospholipid bilayers with the TIP4P/2005 water model. I have downloaded in the Klauda's website several bilayer starting conformations. However, since CHARMM uses the TIP3 water model, I am confused to convert the water coordinates into a water four sites. Does somebody has a little script to share with me that can help me? Thank you for kindly help Stephane -- 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] script to convert the TIP3P water model into TIP4
Hello, Because I want to compare the simulation results (essentially water dynamic) with previous simulations of reverse micelles, micelles carried out with the same water model. Stephane -- Message: 8 Date: Mon, 23 Sep 2013 10:45:56 +0200 From: Dr. Vitaly Chaban vvcha...@gmail.com Subject: Re: [gmx-users] script to convert the TIP3P water model into TIP4P To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: capxdd+alyfc4g+wnzj7bk0+rj3eexj_js7stjtdwymayt5t...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 I am confused. Why do you want 4-sites water? Dr. Vitaly V. Chaban On Mon, Sep 23, 2013 at 10:36 AM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello all, It is not a gromacs problem per se, but I hope that some gromacs users can help me. I would to do simulations of phospholipid bilayers with the TIP4P/2005 water model. I have downloaded in the Klauda's website several bilayer starting conformations. However, since CHARMM uses the TIP3 water model, I am confused to convert the water coordinates into a water four sites. Does somebody has a little script to share with me that can help me? Thank you for kindly help Stephane -- 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] trjconv and Floating point exception
Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely get the following error: Select a group: 0 Selected 0: 'System' Reading frame 0 time0.000 Precision of traj.xtc is 0.004 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up confout.gro to ./#confout.gro.1# Reading frame 17000 time 510.000 Floating point exception (core dumped) What is it because of? Insufficient memory? Or something with the trajectory file (it works nice if -dump 20). The traj.xtc file is 11GB, the memory is 64GB. Thanks! Dr. Vitaly V. Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization
On 9/23/13 3:08 AM, marzieh dehghan wrote: Hi every body in order to protein- ligand docking, energy minimization was done by GROMACS. I did the following steps for insulin pdb file: 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce 2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr 3-mdrun -v -deffnm em 4- editconf -f em.gro -o final.pdb -c -d 1.0 -bt cubic everything was perfect, but the final pdb file has two problems: 1- chain ID was missed. Chain IDs are irrelevant in Gromacs, but can be restored by converting file formats using trjconv and a .tpr file. 2- insulin contains two chains (A B) which connect by disulfide bond, but after energy minimization, two chains are separated. This may or may not be a simple PBC effect (again, fixed with trjconv). If the bond exists in the topology, it cannot be broken. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gmx-users Digest, Vol 113, Issue 101
On 9/23/13 3:28 AM, Jonathan Saboury wrote: That said, there is an spc.itp within the AMBER subdirectories that needs to be #included more explicitly, i.e. #include amber99sb.ff/spc.itp May I ask why you are using SPC? The AMBER force fields were parametrized with TIP3P, so I see no viable reason to use a different water model. Ah, fixed and works like a charm, thank you :) To be completely honest I was using it out of ignorance. I've just been checking what has worked for me in tutorials and been working from there to something I am more interested in. Tutorials are designed to be self-consistent (well, at least mine are) so you can't pick and choose. If you change something, you risk invalidating everything, depending on what it is that you change. It's not a bug, because genbox does not advertise such a feature. genbox is hard-coded to only ever deal with water. Anything else is up to the user. Interesting, any reason a user would not want such a feature? There are plenty of reasons to want it, but no one's taken the time to actually do it because the demand hasn't been high. If you want something in the code, file a feature request on redmine.gromacs.org, or even better, propose the patch yourself :) Any force field can be parametrized to give correct target data, especially for a molecule as simple as cyclohexane. What I use is a complex question, because it depends entirely upon the task at hand :) Can you list a few so I can go check them out on my own? It would be appreciated :) This is really a topic that can span textbook chapters. Any attempt at a list would be woefully inadequate. The best advice I can give is to read about different force fields and how they are applied to different molecules of interest. Email cannot do the topic justice; studying the literature can. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] script to convert the TIP3P water model into TIP4
On 9/23/13 5:02 AM, ABEL Stephane 175950 wrote: Hello, Because I want to compare the simulation results (essentially water dynamic) with previous simulations of reverse micelles, micelles carried out with the same water model. The math for producing the virtual site in TIP4P is described in tip4p.itp, so you can use that. What's more curious is that if a paper claims to use TIP4P but the provided files use TIP3P, then either there has been a mix-up in the files or an error in the paper. In either case, I find it odd to use TIP4P with CHARMM, especially given the sensitivity of lipid parameters to the water model. Without knowing the paper you're talking about, I will not criticize the choice as it may have been justified. It's probably a good question to ask of the corresponding author of the study you are trying to reproduce. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 and Floating point exception
On 9/23/13 6:41 AM, Dr. Vitaly Chaban wrote: Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely get the following error: Select a group: 0 Selected 0: 'System' Reading frame 0 time0.000 Precision of traj.xtc is 0.004 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up confout.gro to ./#confout.gro.1# Reading frame 17000 time 510.000 Floating point exception (core dumped) Looks like a corruption in the trajectory. What does gmxcheck say about traj.xtc? Can you bypass the frame using -b and dump out the desired frame? -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: Re: Calculation of binding enthalpy in vacuum
Dear Vitaly, Thank you for your suggestion. I have also tried calculating interaction energies by specifying energygrps in .mdp file, but calculated energies deviate greatly from QM calculated energies and experimental results. I suspect that the structure of each component in complex differs from the structures when they were alone, because this will lead to a deviation in equilibrium binding enthalpy from the interaction energies that is calculated with energygrps line in .mdp file. My guest of interest have two charges at a short distance, which is very unfavorable and the charges will try to be furthest apart. However, my host molecule can stability the charges via oppositely charged groups, and so now the guest molecule forms a bent structure. In this case, shouldn't the change in energy due to the different conformation of the guest be taken into account, to discuss equilibrium binding enthalpy? I feel maybe this wouldn't be well represented with interaction energies. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Re: Calculation of binding enthalpy in vacuum
On Mon, Sep 23, 2013 at 2:40 PM, Jong Wha Lee jongwh...@postech.ac.kr wrote: Dear Vitaly, Thank you for your suggestion. I have also tried calculating interaction energies by specifying energygrps in .mdp file, but calculated energies deviate greatly from QM calculated energies and experimental results. I suspect that the structure of each component in complex differs from the structures when they were alone, because this will lead to a deviation in equilibrium binding enthalpy from the interaction energies that is calculated with energygrps line in .mdp file. This might be because of electrostatics treatment method. Use simple cut-off scheme and specify a really large cut-off radius, which exceeds the sum of the sizes of your binding particles. I made tons of such comparisons, QM vs. MM. It works pretty well. My guest of interest have two charges at a short distance, which is very unfavorable and the charges will try to be furthest apart. However, my host molecule can stability the charges via oppositely charged groups, and so now the guest molecule forms a bent structure. In this case, shouldn't the change in energy due to the different conformation of the guest be taken into account, to discuss equilibrium binding enthalpy? I feel maybe this wouldn't be well represented with interaction energies. The binding energy is an energy gain, dE, in the following reaction A + B - AB, dE A, B, and AB are optimized geometries: in vacuum, in solvent or anywhere. So, if a molecule changes its conformation during binding, this energy gain/loss should be a part of the binding energy, I see no methodological problem here. Dr. Vitaly V. Chaban -- 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] Funky output trajectory (lines all over the place)
On Sep 23, 2013 9:23 AM, Jonathan Saboury jsab...@gmail.com wrote: I tried minimizing a box of cyclohexanes and water. The first frame is fine, but after that seemingly random lines form in vmd with the cyclohexanes. The waters seem to minimizing just fine though. I am sure I am just doing something extremely silly and I just don't know it because of ignorance. I have no formal training on simulations, you are my only hope! Google is pretty useful, too ;-) http://www.gromacs.org/Documentation/FAQsdeals with this kind of issue. Mark Perhaps using the em.gro with the em.trr is not the correct way to visualize? I used the command: vmd em.gro em.trr Or something is wrong with my em.mdp? em.mdp: http://pastebin.com/raw.php?i=LPPN5xRF Commands used: http://pastebin.com/raw.php?i=Jk0fKLJj Here are all the files, in case you need them: http://www.sendspace.com/file/gx8j97 Sorry for dumping all of this, but I am genuinely stuck. I've tried reading about the mdp file format but i only understand ~5%. If I could have done more I would have tried :/ Thank you all, it is really appreciated. -Jonathan Saboury -- 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] energy minimization
On Sep 23, 2013 9:08 AM, marzieh dehghan dehghanmarz...@gmail.com wrote: Hi every body in order to protein- ligand docking, energy minimization was done by GROMACS. I did the following steps for insulin pdb file: 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce 2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr 3-mdrun -v -deffnm em 4- editconf -f em.gro -o final.pdb -c -d 1.0 -bt cubic everything was perfect, but the final pdb file has two problems: 1- chain ID was missed. 2- insulin contains two chains (A B) which connect by disulfide bond, but after energy minimization, two chains are separated. Did pdb2gmx even report it being made? Mark I would like to know how to solve these problems? best regards -- *Marzieh Dehghan PhD Candidate of Biochemistry Institute of biochemistry and Biophysics (IBB) University of Tehran, Tehran- Iran.* -- 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] script to convert the TIP3P water model into TIP4(P)/2005
Hello Justin, Thank you for your response and your interest for my simulations ;) I am of course aware that the primary water model for the CHARMM is the TIP3(S)P model. Since, I am mainly interested to the water dynamic around DOPC molecules in the context of the different water/DOPC mesophases (not data available, I currently doing the tests ;)) and that it is known that the TIP4P/2005 water model (it is the model, I want to use) reproduces better the water dynamic and structure than the TIP3P water model, I would like to test if the TIP4P/2005 water can be used in simulation of membranes. I am not aware that somebody have already done the test. Finally, Justin, you are probably right here, the results will be probably not good as it is suggested by Pastor and MacKerell in their paper for TIP4P-EW water model [1], but I think that it is worth a test to confirm this in case of the TIP4P/2005. I am not the first one to ask this question in the context of simulations with the CHARMM force field (for protein, here [2]). [1] www.ncbi.nlm.nih.gov/pmc/articles/PMC3133452/ [2] Nutt, D. R.; Smith, J. C. Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied? J. Chem. Theory Comput. 2007, 3, 1550–1560. Stephane On 9/23/13 5:02 AM, ABEL Stephane 175950 wrote: Hello, Because I want to compare the simulation results (essentially water dynamic) with previous simulations of reverse micelles, micelles carried out with the same water model. The math for producing the virtual site in TIP4P is described in tip4p.itp, so you can use that. What's more curious is that if a paper claims to use TIP4P but the provided files use TIP3P, then either there has been a mix-up in the files or an error in the paper. In either case, I find it odd to use TIP4P with CHARMM, especially given the sensitivity of lipid parameters to the water model. Without knowing the paper you're talking about, I will not criticize the choice as it may have been justified. It's probably a good question to ask of the corresponding author of the study you are trying to reproduce. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] The charge of cofactor and ligand
Dear prof, can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then use acpype to generate GAFF force field parameter for the NAD+ and ligand? -- 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 and Floating point exception
On 9/23/13 11:39 AM, Dr. Vitaly Chaban wrote: Dr. Vitaly V. Chaban On Mon, Sep 23, 2013 at 2:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/23/13 6:41 AM, Dr. Vitaly Chaban wrote: Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely get the following error: Select a group: 0 Selected 0: 'System' Reading frame 0 time0.000 Precision of traj.xtc is 0.004 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up confout.gro to ./#confout.gro.1# Reading frame 17000 time 510.000 Floating point exception (core dumped) Looks like a corruption in the trajectory. What does gmxcheck say about traj.xtc? gmxcheck -f traj.xtc Reading frame 17000 time 510.000 Killed Can you bypass the frame using -b and dump out the desired frame? No. The process comes to 5.1 ms and is killed. All available evidence then suggests you have a corrupted frame about a third of the way through the trajectory. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] The charge of cofactor and ligand
How do GAFF and acpype work? Mark On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong aixintiank...@126.com wrote: Dear prof, can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then use acpype to generate GAFF force field parameter for the NAD+ and ligand? -- 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] Regarding g_sgangle index file
Hi, On Thu, Sep 19, 2013 at 7:19 PM, Venkat Reddy venkat...@gmail.com wrote: @Teemu Murtola: Are there any modifications to the other gmx tools? (eg: rdf calculation with dynamic selection...etc). I am trying to explore the new version. Unfortunately, there are currently very few tools using the new mechanisms. http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 lists most of the changes: in practice, there's 'gmx distance' as a more flexible alternative to computing distances, and g_select (now 'gmx select') has gotten a few extra output options. There's also at least one new tool, 'gmx freevolume'. Best regards, Teemu -- 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] confusion about implicint solvent
Good afternoon everybody, I'm a bit confuse about gromacs performances with implicit solvent. I'm simulating a 1000 residues protein with explicit solvent, using both a cpu and a gpu cluster. With a gpu node (12 cores and 3 M2090 gpu ) I reach 10 ns/day, while with no gpu and 144 cores I got 34 ns/day. Because I have several mutants (more than 50) I have to reduce the average simulation time and I was considering different option such as the use of implicit solvent. I tried with both the clusters and using gromacs 4.6 and 4.5 but the performances are terrible (1 day for 100ps) comparing to the explicit solvent. I read all the other messages on the mailing-list and the documentation, but the mix of old and new features/posts really confuses me a lot. Here (http://www.gromacs.org/Documentation/Acceleration_and_parallelization) it is said that with the gpu 4.5 and implicit solvent I should expect a substantial speedup. Here ( http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM#Benchmark_results.3a_GROMACS_CPU_vs_GPU ) I found this sentence It is ultimately up to you as a user to decide what simulations setups to use, but we would like to emphasize the simply amazing implicit solvent performance provided by GPUs. I follow the advise found in the mailing list and read both the documentation (site and manual), but I can't figured it out what should I do. How can you guys have amazing performances? I also found this answer from a last March post (http://gromacs.5086.x6.nabble.com/Implicit-solvent-MD-is-not-fast-and-not-accurate-td5006659.html#none) that confuses me even more. Performance issues are known. There are plans to implement the implicit solvent code for GPU and perhaps allow for better parallelization, but I don't know what the status of all that is. As it stands (and as I have said before on this list and to the developers privately), the implicit code is largely unproductive because the performance is terrible. Should I skip the idea of using implicit solvent and try something else? these are a set of parameters that I used (also the -pd flag) ; Run parameters integrator = sd tinit = 0 nsteps = 5 dt= 0.002 ; Output control nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout= 5000 xtc_precision = 1000 energygrps = system ; Bond parameters continuation= no constraints = all-bonds constraint_algorithm = lincs lincs_iter = 1 lincs_order = 4 lincs_warnangle = 30 ; Neighborsearching ns_type = simple nstlist = 0 rlist= 0 rcoulomb= 0 rvdw = 0 ; Electrostatics coulombtype = cut-off pbc= no comm_mode= Angular implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii = 0 gb_epsilon_solvent= 80 gb_dielectric_offset= 0.009 sa_algorithm = Ace-approximation sa_surface_tension= 0.0054 ; Temperature coupling tcoupl= v-rescale tc_grps = System tau_t = 0.1 ref_t = 310 ; Velocity generation gen_vel= yes ld_seed= -1 thank you for the help. cheers Francesco -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme
On 9/20/13 7:59 AM, Mark Abraham wrote: Note that the group scheme does not reproduce the (AFAIK unpublished) CHARMM switching scheme, either. In case anyone is interested, the reference cited in the CHARMM papers for the switching and shifting functions is dx.doi.org/10.1002/jcc.540150702. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] confusion about implicint solvent
Hi, Admittedly, both the documentation on these features and the communication on the known issues with these aspects of GROMACS has been lacking. Here's a brief summary/explanation: - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu which is essentially mdrun + OpenMM, hence it has some limitations, most notably it can only run on a single GPU. The performance, depending on setting, can be up to 10x higher than on the CPU. - GROMACS 4.6: the native GPU acceleration does supports only explicit solvent, mdrun + OpenMM is still available (exactly for implicit solvent runs), but has been moved to the contrib section which means that it is not fully supported. Moreover, OpenMM support - unless somebody volunteers for maintenance of the mdrun-OpenMM interface - will be dropped in the next release. I can't comment much on the implicit solvent code on the CPU side other than the fact that there have been issues which AFAIK limit the parallelization to a rather small number of cores, hence the achievable performance is also limited. I hope others can clarify this aspect. Cheers, -- Szilárd On Mon, Sep 23, 2013 at 7:34 PM, Francesco frac...@myopera.com wrote: Good afternoon everybody, I'm a bit confuse about gromacs performances with implicit solvent. I'm simulating a 1000 residues protein with explicit solvent, using both a cpu and a gpu cluster. With a gpu node (12 cores and 3 M2090 gpu ) I reach 10 ns/day, while with no gpu and 144 cores I got 34 ns/day. Because I have several mutants (more than 50) I have to reduce the average simulation time and I was considering different option such as the use of implicit solvent. I tried with both the clusters and using gromacs 4.6 and 4.5 but the performances are terrible (1 day for 100ps) comparing to the explicit solvent. I read all the other messages on the mailing-list and the documentation, but the mix of old and new features/posts really confuses me a lot. Here (http://www.gromacs.org/Documentation/Acceleration_and_parallelization) it is said that with the gpu 4.5 and implicit solvent I should expect a substantial speedup. Here ( http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM#Benchmark_results.3a_GROMACS_CPU_vs_GPU ) I found this sentence It is ultimately up to you as a user to decide what simulations setups to use, but we would like to emphasize the simply amazing implicit solvent performance provided by GPUs. I follow the advise found in the mailing list and read both the documentation (site and manual), but I can't figured it out what should I do. How can you guys have amazing performances? I also found this answer from a last March post (http://gromacs.5086.x6.nabble.com/Implicit-solvent-MD-is-not-fast-and-not-accurate-td5006659.html#none) that confuses me even more. Performance issues are known. There are plans to implement the implicit solvent code for GPU and perhaps allow for better parallelization, but I don't know what the status of all that is. As it stands (and as I have said before on this list and to the developers privately), the implicit code is largely unproductive because the performance is terrible. Should I skip the idea of using implicit solvent and try something else? these are a set of parameters that I used (also the -pd flag) ; Run parameters integrator = sd tinit = 0 nsteps = 5 dt= 0.002 ; Output control nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout= 5000 xtc_precision = 1000 energygrps = system ; Bond parameters continuation= no constraints = all-bonds constraint_algorithm = lincs lincs_iter = 1 lincs_order = 4 lincs_warnangle = 30 ; Neighborsearching ns_type = simple nstlist = 0 rlist= 0 rcoulomb= 0 rvdw = 0 ; Electrostatics coulombtype = cut-off pbc= no comm_mode= Angular implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii = 0 gb_epsilon_solvent= 80 gb_dielectric_offset= 0.009 sa_algorithm = Ace-approximation sa_surface_tension= 0.0054 ; Temperature coupling tcoupl= v-rescale tc_grps = System tau_t = 0.1 ref_t = 310 ; Velocity generation gen_vel= yes ld_seed= -1 thank you for the help. cheers Francesco -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] script to convert the TIP3P water model into TIP4(P)/2005
On 9/23/13 10:23 AM, ABEL Stephane 175950 wrote: Hello Justin, Thank you for your response and your interest for my simulations ;) I am of course aware that the primary water model for the CHARMM is the TIP3(S)P model. Since, I am mainly interested to the water dynamic around DOPC molecules in the context of the different water/DOPC mesophases (not data available, I currently doing the tests ;)) and that it is known that the TIP4P/2005 water model (it is the model, I want to use) reproduces better the water dynamic and structure than the TIP3P water model, I would like to test if the TIP4P/2005 water can be used in simulation of membranes. I am not aware that somebody have already done the test. Finally, Justin, you are probably right here, the results will be probably not good as it is suggested by Pastor and MacKerell in their paper for TIP4P-EW water model [1], but I think that it is worth a test to confirm this in case of the TIP4P/2005. I am not the first one to ask this question in the context of simulations with the CHARMM force field (for protein, here [2]). [1] www.ncbi.nlm.nih.gov/pmc/articles/PMC3133452/ [2] Nutt, D. R.; Smith, J. C. Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied? J. Chem. Theory Comput. 2007, 3, 1550–1560. It sounds like you're on the right track, at least knowing that a considerable amount of work has to be done to prove that the force field + water model combination is sound. Given that you're going to have to re-equilibrate the water anyway, I don't see why you have to start with TIP3P and try to hack it into becoming TIP4P; I would just strip the water and re-solvate. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] confusion about implicint solvent
On 9/23/13 2:08 PM, Szilárd Páll wrote: Hi, Admittedly, both the documentation on these features and the communication on the known issues with these aspects of GROMACS has been lacking. Here's a brief summary/explanation: - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu which is essentially mdrun + OpenMM, hence it has some limitations, most notably it can only run on a single GPU. The performance, depending on setting, can be up to 10x higher than on the CPU. - GROMACS 4.6: the native GPU acceleration does supports only explicit solvent, mdrun + OpenMM is still available (exactly for implicit solvent runs), but has been moved to the contrib section which means that it is not fully supported. Moreover, OpenMM support - unless somebody volunteers for maintenance of the mdrun-OpenMM interface - will be dropped in the next release. I can't comment much on the implicit solvent code on the CPU side other than the fact that there have been issues which AFAIK limit the parallelization to a rather small number of cores, hence the achievable performance is also limited. I hope others can clarify this aspect. I never got the implicit code to run on more than 2 CPUs, and as I recall Berk hard-coded this due to a limitation involving constraints. It's been a couple years since I tried anything with implicit since (1) the OpenMM support was so buggy and incomplete on GPU and (2) the code ran an order of magnitude slower on CPU than the explicit solvent counterpart. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 : gmx-users Digest, Vol 113, Issue 106
Finally, I have resolved my (little) problem: I used CHARMM-GUI to constructed the membrane, removed the TIP3 water molecules and then resolvate the bilayer with TIP4P/2005 water molecules. The simulation seems to work. Stephane On 9/23/13 10:23 AM, ABEL Stephane 175950 wrote: Hello Justin, Thank you for your response and your interest for my simulations ;) I am of course aware that the primary water model for the CHARMM is the TIP3(S)P model. Since, I am mainly interested to the water dynamic around DOPC molecules in the context of the different water/DOPC mesophases (not data available, I currently doing the tests ;)) and that it is known that the TIP4P/2005 water model (it is the model, I want to use) reproduces better the water dynamic and structure than the TIP3P water model, I would like to test if the TIP4P/2005 water can be used in simulation of membranes. I am not aware that somebody have already done the test. Finally, Justin, you are probably right here, the results will be probably not good as it is suggested by Pastor and MacKerell in their paper for TIP4P-EW water model [1], but I think that it is worth a test to confirm this in case of the TIP4P/2005. I am not the first one to ask this question in the context of simulations with the CHARMM force field (for protein, here [2]). [1] www.ncbi.nlm.nih.gov/pmc/articles/PMC3133452/ [2] Nutt, D. R.; Smith, J. C. Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied? J. Chem. Theory Comput. 2007, 3, 1550?1560. It sounds like you're on the right track, at least knowing that a considerable amount of work has to be done to prove that the force field + water model combination is sound. Given that you're going to have to re-equilibrate the water anyway, I don't see why you have to start with TIP3P and try to hack it into becoming TIP4P; I would just strip the water and re-solvate. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 and Floating point exception
Dr. Vitaly V. Chaban On Mon, Sep 23, 2013 at 2:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/23/13 6:41 AM, Dr. Vitaly Chaban wrote: Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely get the following error: Select a group: 0 Selected 0: 'System' Reading frame 0 time0.000 Precision of traj.xtc is 0.004 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up confout.gro to ./#confout.gro.1# Reading frame 17000 time 510.000 Floating point exception (core dumped) Looks like a corruption in the trajectory. What does gmxcheck say about traj.xtc? gmxcheck -f traj.xtc Reading frame 17000 time 510.000 Killed Can you bypass the frame using -b and dump out the desired frame? No. The process comes to 5.1 ms and is killed. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] g_energy
Hello. I was calculating the viscosity of hexane through the Gromacs command g_energy. Three files are generated: visco.xvg, evisco.xvg and eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but the value does not match the experimental. I used 8 ns simulation at equilibrium. However, the file evisco.xvg has a value very close to the experimental but has only a time of 2 ns (version 4.0.7). Why? Furthermore, I want to know what is present in the file eviscoi.xvg. Thank you. http://help-gromacs.blogspot.com.br/2013/09/viscosidade-gromacs-407.html -- 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: Charmm 36 forcefield with verlet cut-off scheme
With what was said: what do you all think of the following parameters for Charmm 36: rlist = 1.2 rlistlong = 1.4 vdwtype = cutoff rvdw-switch = 1.0 rvdw = 1.2 rcouloumb = 1.2 vdw-modifier = Potential-shift-Verlet DispCorr = No cutoff-scheme = Verlet -- View this message in context: http://gromacs.5086.x6.nabble.com/Charmm-36-forcefield-with-verlet-cut-off-scheme-tp5011322p5011413.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] confusion about implicint solvent
On Mon, Sep 23, 2013 at 8:08 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: Hi, Admittedly, both the documentation on these features and the communication on the known issues with these aspects of GROMACS has been lacking. Here's a brief summary/explanation: - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu which is essentially mdrun + OpenMM, hence it has some limitations, most notably it can only run on a single GPU. The performance, depending on setting, can be up to 10x higher than on the CPU. - GROMACS 4.6: the native GPU acceleration does supports only explicit solvent, mdrun + OpenMM is still available (exactly for implicit solvent runs), but has been moved to the contrib section which means that it is not fully supported. Moreover, OpenMM support - unless somebody volunteers for maintenance of the mdrun-OpenMM interface - will be dropped in the next release. I can't comment much on the implicit solvent code on the CPU side other than the fact that there have been issues which AFAIK limit the parallelization to a rather small number of cores, hence the achievable performance is also limited. I hope others can clarify this aspect. IIRC the best 4.5 performance for CPU-only implicit solvent used infinite cut-offs and SIMD acceleration. The SIMD is certainly broken in 4.6 (and IIRC was explicitly disabled at some point after 4.6.3). There is limited enthusiasm for fixing things (e.g. see parts of http://redmine.gromacs.org/issues/1292) but nobody with the skills has so far applied the time to do so. As always with an open-source project, if you want something, be prepared to roll up your sleeves and work, or hit your knees and pray! :-) Mark Cheers, -- Szilárd On Mon, Sep 23, 2013 at 7:34 PM, Francesco frac...@myopera.com wrote: Good afternoon everybody, I'm a bit confuse about gromacs performances with implicit solvent. I'm simulating a 1000 residues protein with explicit solvent, using both a cpu and a gpu cluster. With a gpu node (12 cores and 3 M2090 gpu ) I reach 10 ns/day, while with no gpu and 144 cores I got 34 ns/day. Because I have several mutants (more than 50) I have to reduce the average simulation time and I was considering different option such as the use of implicit solvent. I tried with both the clusters and using gromacs 4.6 and 4.5 but the performances are terrible (1 day for 100ps) comparing to the explicit solvent. I read all the other messages on the mailing-list and the documentation, but the mix of old and new features/posts really confuses me a lot. Here (http://www.gromacs.org/Documentation/Acceleration_and_parallelization) it is said that with the gpu 4.5 and implicit solvent I should expect a substantial speedup. Here ( http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM#Benchmark_results.3a_GROMACS_CPU_vs_GPU ) I found this sentence It is ultimately up to you as a user to decide what simulations setups to use, but we would like to emphasize the simply amazing implicit solvent performance provided by GPUs. I follow the advise found in the mailing list and read both the documentation (site and manual), but I can't figured it out what should I do. How can you guys have amazing performances? I also found this answer from a last March post (http://gromacs.5086.x6.nabble.com/Implicit-solvent-MD-is-not-fast-and-not-accurate-td5006659.html#none) that confuses me even more. Performance issues are known. There are plans to implement the implicit solvent code for GPU and perhaps allow for better parallelization, but I don't know what the status of all that is. As it stands (and as I have said before on this list and to the developers privately), the implicit code is largely unproductive because the performance is terrible. Should I skip the idea of using implicit solvent and try something else? these are a set of parameters that I used (also the -pd flag) ; Run parameters integrator = sd tinit = 0 nsteps = 5 dt= 0.002 ; Output control nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout= 5000 xtc_precision = 1000 energygrps = system ; Bond parameters continuation= no constraints = all-bonds constraint_algorithm = lincs lincs_iter = 1 lincs_order = 4 lincs_warnangle = 30 ; Neighborsearching ns_type = simple nstlist = 0 rlist= 0 rcoulomb= 0 rvdw = 0 ; Electrostatics coulombtype = cut-off pbc= no comm_mode= Angular implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii = 0 gb_epsilon_solvent= 80 gb_dielectric_offset= 0.009
Re: [gmx-users] confusion about implicint solvent
On 2013-09-23 20:23, Justin Lemkul wrote: On 9/23/13 2:08 PM, Szilárd Páll wrote: Hi, Admittedly, both the documentation on these features and the communication on the known issues with these aspects of GROMACS has been lacking. Here's a brief summary/explanation: - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu which is essentially mdrun + OpenMM, hence it has some limitations, most notably it can only run on a single GPU. The performance, depending on setting, can be up to 10x higher than on the CPU. - GROMACS 4.6: the native GPU acceleration does supports only explicit solvent, mdrun + OpenMM is still available (exactly for implicit solvent runs), but has been moved to the contrib section which means that it is not fully supported. Moreover, OpenMM support - unless somebody volunteers for maintenance of the mdrun-OpenMM interface - will be dropped in the next release. I can't comment much on the implicit solvent code on the CPU side other than the fact that there have been issues which AFAIK limit the parallelization to a rather small number of cores, hence the achievable performance is also limited. I hope others can clarify this aspect. I never got the implicit code to run on more than 2 CPUs, and as I recall Berk hard-coded this due to a limitation involving constraints. It's been a couple years since I tried anything with implicit since (1) the OpenMM support was so buggy and incomplete on GPU and (2) the code ran an order of magnitude slower on CPU than the explicit solvent counterpart. -Justin And finally, even though this is not what you were asking, and likely not wanted to hear either: with implicit solvent your results will not be general enough to be useful, if e.g. hydrogen bonds are important. I would like to recommend my latest paper which shows how solvent entropy and enthalpy contribute in a complex manner to non-bonded interactions in a way that implicit solvent never could: http://pubs.acs.org/doi/abs/10.1021/ct400404q -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:gmx-users Digest, Vol 113, Issue 106
Dear, First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negative. so i copy the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber and then replace the AM1-BCC with the resp charge formhttp://www.pharmacy.manchester.ac.uk/bryce/amber . At last, i use acpype –i ben.mol2 –c user to get the nad.itp file. so the NAD+ use the RESP charge and the ligand use the AM1-BCC charges , can i do like this ? i use this method to get the NAD+.itp file? is correct or not ? At 2013-09-24 02:24:20,gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: The charge of cofactor and ligand (Mark Abraham) 2. Re: Regarding g_sgangle index file (Teemu Murtola) 3. g_energy (Marcelo Vanean) 4. Re: confusion about implicint solvent (Szil?rd P?ll) 5. Re: Re: Charmm 36 forcefield with verlet cut-off scheme (Justin Lemkul) 6. Re: script to convert the TIP3P water model into TIP4(P)/2005 (Justin Lemkul) 7. Re: confusion about implicint solvent (Justin Lemkul) -- Message: 1 Date: Mon, 23 Sep 2013 19:40:23 +0200 From: Mark Abraham mark.j.abra...@gmail.com Subject: Re: [gmx-users] The charge of cofactor and ligand To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: camnumat5bsq5xzr-q0zu27bt0hma2m9wauduf-6lk+dn1ss...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 How do GAFF and acpype work? Mark On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong aixintiank...@126.com wrote: Dear prof, can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then use acpype to generate GAFF force field parameter for the NAD+ and ligand? -- 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] Re: Re: Re: Calculation of binding enthalpy in
Dear Vitaly, Thank you very much for your reply. I originally asked the question because I wasn't sure my values were from correct procedures. Now I see how I could properly calculate binding energies with MM. John Lee Dear Vitaly, Thank you for your suggestion. I have also tried calculating interaction energies by specifying energygrps in .mdp file, but calculated energies deviate greatly from QM calculated energies and experimental results. I suspect that the structure of each component in complex differs from the structures when they were alone, because this will lead to a deviation in equilibrium binding enthalpy from the interaction energies that is calculated with energygrps line in .mdp file. This might be because of electrostatics treatment method. Use simple cut-off scheme and specify a really large cut-off radius, which exceeds the sum of the sizes of your binding particles. I made tons of such comparisons, QM vs. MM. It works pretty well. My guest of interest have two charges at a short distance, which is very unfavorable and the charges will try to be furthest apart. However, my host molecule can stability the charges via oppositely charged groups, and so now the guest molecule forms a bent structure. In this case, shouldn't the change in energy due to the different conformation of the guest be taken into account, to discuss equilibrium binding enthalpy? I feel maybe this wouldn't be well represented with interaction energies. The binding energy is an energy gain, dE, in the following reaction A + B - AB, dE A, B, and AB are optimized geometries: in vacuum, in solvent or anywhere. So, if a molecule changes its conformation during binding, this energy gain/loss should be a part of the binding energy, I see no methodological problem here. Dr. Vitaly V. Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme
On 9/23/13 4:04 PM, akk5r wrote: With what was said: what do you all think of the following parameters for Charmm 36: rlist = 1.2 rlistlong = 1.4 vdwtype = cutoff rvdw-switch = 1.0 rvdw = 1.2 rcouloumb = 1.2 vdw-modifier = Potential-shift-Verlet DispCorr = No cutoff-scheme = Verlet rvdw-switch has no effect here, and I have no real hard evidence to know whether or not this will produce the same effect as the traditional settings. You would have to carefully demonstrate that what you're doing doesn't break the force field. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] The charge of cofactor and ligand
On 9/23/13 5:10 PM, aixintiankong wrote: Dear, First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negative. so i copy the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber and then replace the AM1-BCC with the resp charge formhttp://www.pharmacy.manchester.ac.uk/bryce/amber . At last, i use acpype –i ben.mol2 –c user to get the nad.itp file. so the NAD+ use the RESP charge and the ligand use the AM1-BCC charges , can i do like this ? i use this method to get the NAD+.itp file? is correct or not ? Why not just use the parameters that are already published? Unless there's something wrong with them, there's no need to reinvent the wheel. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: Fatal Error: Residue 'DMP' not found in residue topology database
Justin.. I understand the problem.. But.. How to generate a .rtp file myself.. - Santhosh Kumar Nagarajan MTech Bioinformatics SRM University Chennai India -- View this message in context: http://gromacs.5086.x6.nabble.com/Fatal-Error-Residue-DMP-not-found-in-residue-topology-database-tp5011333p5011420.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Regarding g_sgangle index file
Hello Sir, I have been using the new tool gmx gangle. My actual intention is to calculate the orientation between any two same molecules (say cholesterol) throughout the trajectory and there are 40 cholesterol molecules. But I couldn't calculate it. I am getting 0 as output. My command is: gmx gangle -f traj_noPBC.xtc -s topol.tpr -n -g1 vector -g2 vector -group1 'resname CHOL and name R5 R0' -group2 'resname CHOL and name R5 R0' -oav -oall -oh On Mon, Sep 23, 2013 at 11:19 PM, Teemu Murtola teemu.murt...@gmail.comwrote: Hi, On Thu, Sep 19, 2013 at 7:19 PM, Venkat Reddy venkat...@gmail.com wrote: @Teemu Murtola: Are there any modifications to the other gmx tools? (eg: rdf calculation with dynamic selection...etc). I am trying to explore the new version. Unfortunately, there are currently very few tools using the new mechanisms. http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 lists most of the changes: in practice, there's 'gmx distance' as a more flexible alternative to computing distances, and g_select (now 'gmx select') has gotten a few extra output options. There's also at least one new tool, 'gmx freevolume'. Best regards, Teemu -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
