Re: [gmx-users] OPLS/AA + TIP5P, anybody?
Dear Chris, Thank you for your message. I uploaded everything to the redmine. I will let you know how the simulation with generated velocities went. I asked the authors about any exemplary input that worked with tip5p and oplsaa, but I did not get anything... Best, Grzegorz On 2013-10-04 17:20, Christopher Neale wrote: Dear Grzegorz: From a quick look at your .mdp, I also suggest that you go back to your system including the peptide that you had managed to finish EM with modified flexible tip5p but then crashed with the standard rigid tip5p during MD and try the MD again using gen-vel = yes if you're still seeing problems, why not upload your water-only system and your with-small-peptide test system to redmine. It's meant as a place to start a discussion, share files, and help us not to foget about a problem that may exist, so I am not sure why you hesitate. Also, you said that the authors of that other OPLS-Tip5p paper had no problems. You might ask them for .gro .mdp and .top files so that you can see exactly what they did and how it differs from what you are doing. Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS/AA + TIP5P, anybody?
Dear Chris, By now 7ns of the MD passed without a single warning. Best Regards, Grzegorz P.s. The mdp: constraints = none integrator = md dt = 0.001; ps nsteps = 1000 ; total 10 ns nstcomm = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 25 xtc_grps= System nstlog = 1000 nstenergy = 1000 nstlist = 20 ns_type = grid rlist = 1.3 coulombtype = PME fourierspacing = 0.1 pme_order = 4 optimize_fft= yes rcoulomb= 1.3 rvdw= 1.3 vdwtype = cut-off pbc = xyz DispCorr= EnerPres Tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t = 0.1 ref_t = 300.0 pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no cutoff-scheme = Verlet On 2013-09-30 21:47, Christopher Neale wrote: One a system passes EM and a couple of ps of MD, is it always stable indefinitely? If not, then something is wrong somewhere. -- original message -- Dear Chris, I put one tip5p molecule in a center of dodecahedral box - 2nm from that molecule to walls, filled it with tip5p, ran 6000 steps of steep minimization. After another 2704 steps of cg it converged to emtol 1.0. I run 100k steps of nvt on this box afterwards (http://shroom.ibb.waw.pl/tip5p/pure1). But the water is very capricious. If I ran only 2000 steps of steep, the following cg crashed after less than 1000 steps because a water molecule could not be settled. I could not minimize another box, filled only by genbox from an empty gro file (http://shroom.ibb.waw.pl/tip5p/pure2). I understand that you have to have some luck if you run a simulation in pbc with rigid water, which interacts through walls of the box with the other side and was not well placed. Also, I had several segfaults during minimization that I was able to avoid only by limiting the number of cores. I checked distances between OW and LPx on a crashing minimization with a peptide - 2812 water molecules. Maximum force reached 8.8e+24 in 225 steep steps, but all the 5624 distances were rock solid 0.7A, as expected. I still did not post the redmine issue, I want to be sure that I am doing everything correctly. On 2013-09-29 18:47, Christopher Neale wrote: Dear Grzegorz: Under no conditions should any of the tip5p geometry change (for the standard tip5p model). If you find that this is happening, then that is certainly an error. You can check if you like by analyzing your trajectory. However, flexible bonds will allow the distance from the arginine N to the arginine H to vary, which my allow a closer approach of the arginine H to the tip5p dummy site. Did you verify that a water box (no protein) simulates without error? Did you post a redmine issue with .mdp , .gro , and .top files? Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS/AA + TIP5P, anybody?
Dear Chris, Authors answered me very quickly. They did not have such a problem, but I still don't know the details of their input. They used gromacs-3.3, so I decided to give the old one a try. I did some tests with 3.3.4. Although the same problem occurred during steep minimization, some interesting things popped out. When I tried to grompp the system with plain tip5p for cg minimization, it failed: ERROR: can not do Conjugate Gradients with constraints (8484), even though I did not set any constraints. The error is the same for tip4p unless you use flexible model, which tip5p does not have - the water had to be constrained then. I guess that treatment of virtual sites in gromacs-3.3 has something to do with this. I noticed, that constraints make simulations with tip5p more stable. It should not happen, that the LP virtual atoms are pulled further then the defined 0.7 from the oxygen, right? I will keep you updated. Best Regards, Grzegorz On 2013-09-29 04:50, Christopher Neale wrote: Dear Gigo: that's a good comprehensive testing and report. Please let us know what you find out from those authors. Their paper was short on methods (unless I missed it... I didn't check for any SI), so perhaps they did something non-standard and didn't report it. I think at this point it is a good idea for you to file a redmine issue. It's not a gromacs error per se, but if this is true then pdb2gmx or grompp should give a warning or error for the combination of oplsaa and tip5p. Chris. gigo gigo at ibb.waw.pl Sun Sep 29 00:59:42 CEST 2013 Previous message: [gmx-users] OPLS/AA + TIP5P, anybody? Next message: [gmx-users] Restarting simulation -s. files? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Dear Chris, I am really grateful for your help. This is what I did, with additional LJ terms on LP1 and LP2 of tip5p: - 5000 steps of steepest descent with positions restraints on protein and flexible water (flexibility like in tip4p), - 5000 steps of steep, no restraints, flexible water, - 5000 steps of cg, flexible water, - 10 steps of MD with posres and constrained bond lengths, very weak temp coupling (v-rescale), starting without generating of initial velocities, so its heating very slowly to 300K, no pressure coupling - 10 steps of MD with posres, no constraints, v-rescale, nvt - 10 steps of MD, no posres, nvt, - 10 steps of MD, v-rescale, Berendsen pressure coupling, - 10 steps of MD, v-rescale, Parrinello-Rahman pressure coupling. Output of this chain, after removing LJ from LP, became input for 4 simulations just like the last one from the above chain, with or without posres and constraints turned on. Results: 1) Posres off, constraints off : step 0 WARNING: Listed nonbonded interaction between particles 1157 and 1163 == Why does it say particles and not atoms? Nevermind, its lysine on the surface of the protein, one of atoms is dimensionless hydrogen. (...) step 63: Water molecule starting at atom 7923 can not be settled. (...) Segmentation fault 2) Posres off, constraints on : Warning like above + LINCS warnings, all for charged aminoacids on surface of the protein Segfault at step 63 3) Posres on, constraints off, had to add refcoord_scaling = COM : WARNING: Listed nonbonded interaction between particles 3075 and 3079 == arginine on the surface, dimensionless hydrogen 4) Posres on, constraints on, refcoord_scaling = COM : Same warnings, several other positively charged dimensionless hydrogens listed, waters could not be settled, segfault. I tried to run few other peptides and proteins with tip5p, 100% of crashes. Also, tip5p has been used successfully with the charmm foce field: http://pubs.acs.org/doi/abs/10.1021/ct700053u Yes, there are no dimensionless charged hydrogens there except of these on ... tip3p, tip4p and tip5p water. (...) http://pubs.acs.org/doi/abs/10.1021/ct300180w (...) Are you using halogens with oplsaa-x? No, I use OPLSAA distributed with Gromacs. Standard oplsaa (non-x) and tip5p seem to be a fine combination: http://www.sciencedirect.com/science/article/pii/S0006349507713863 you might want to contact the authors of that paper to see if they ever had such problems. Thank you, I will ask them. I am starting to be sure, though, that it is not possible to run any simulations with tip5p and proteins (containing arginine for example) without some tricks, strengthening/constraining bonds at least. It happened during the minimization, that the distance between HHxy and NHx in arginine grew up to 1.48A, while HHxy was landing on LP of the water. Repeatability is 100%. Regards, Grzegorz -- 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
Re: [gmx-users] OPLS/AA + TIP5P, anybody?
Dear Chris, I did not post the redmine issue yet, I want to check every possibility beforehand. I will analyze trajectories more closely now. Best, Grzegorz On 2013-09-29 18:47, Christopher Neale wrote: Dear Grzegorz: Under no conditions should any of the tip5p geometry change (for the standard tip5p model). If you find that this is happening, then that is certainly an error. You can check if you like by analyzing your trajectory. However, flexible bonds will allow the distance from the arginine N to the arginine H to vary, which my allow a closer approach of the arginine H to the tip5p dummy site. Did you verify that a water box (no protein) simulates without error? Did you post a redmine issue with .mdp , .gro , and .top files? Chris. -- original message -- Dear Chris, Authors answered me very quickly. They did not have such a problem, but I still don't know the details of their input. They used gromacs-3.3, so I decided to give the old one a try. I did some tests with 3.3.4. Although the same problem occurred during steep minimization, some interesting things popped out. When I tried to grompp the system with plain tip5p for cg minimization, it failed: ERROR: can not do Conjugate Gradients with constraints (8484), even though I did not set any constraints. The error is the same for tip4p unless you use flexible model, which tip5p does not have - the water had to be constrained then. I guess that treatment of virtual sites in gromacs-3.3 has something to do with this. I noticed, that constraints make simulations with tip5p more stable. It should not happen, that the LP virtual atoms are pulled further then the defined 0.7 from the oxygen, right? I will keep you updated. Best Regards, Grzegorz -- 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] OPLS/AA + TIP5P, anybody?
Dear Chris, I put one tip5p molecule in a center of dodecahedral box - 2nm from that molecule to walls, filled it with tip5p, ran 6000 steps of steep minimization. After another 2704 steps of cg it converged to emtol 1.0. I run 100k steps of nvt on this box afterwards (http://shroom.ibb.waw.pl/tip5p/pure1). But the water is very capricious. If I ran only 2000 steps of steep, the following cg crashed after less than 1000 steps because a water molecule could not be settled. I could not minimize another box, filled only by genbox from an empty gro file (http://shroom.ibb.waw.pl/tip5p/pure2). I understand that you have to have some luck if you run a simulation in pbc with rigid water, which interacts through walls of the box with the other side and was not well placed. Also, I had several segfaults during minimization that I was able to avoid only by limiting the number of cores. I checked distances between OW and LPx on a crashing minimization with a peptide - 2812 water molecules. Maximum force reached 8.8e+24 in 225 steep steps, but all the 5624 distances were rock solid 0.7A, as expected. I still did not post the redmine issue, I want to be sure that I am doing everything correctly. On 2013-09-29 18:47, Christopher Neale wrote: Dear Grzegorz: Under no conditions should any of the tip5p geometry change (for the standard tip5p model). If you find that this is happening, then that is certainly an error. You can check if you like by analyzing your trajectory. However, flexible bonds will allow the distance from the arginine N to the arginine H to vary, which my allow a closer approach of the arginine H to the tip5p dummy site. Did you verify that a water box (no protein) simulates without error? Did you post a redmine issue with .mdp , .gro , and .top files? Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS/AA + TIP5P, anybody?
Dear Chris, I am really grateful for your help. This is what I did, with additional LJ terms on LP1 and LP2 of tip5p: - 5000 steps of steepest descent with positions restraints on protein and flexible water (flexibility like in tip4p), - 5000 steps of steep, no restraints, flexible water, - 5000 steps of cg, flexible water, - 10 steps of MD with posres and constrained bond lengths, very weak temp coupling (v-rescale), starting without generating of initial velocities, so its heating very slowly to 300K, no pressure coupling - 10 steps of MD with posres, no constraints, v-rescale, nvt - 10 steps of MD, no posres, nvt, - 10 steps of MD, v-rescale, Berendsen pressure coupling, - 10 steps of MD, v-rescale, Parrinello-Rahman pressure coupling. Output of this chain, after removing LJ from LP, became input for 4 simulations just like the last one from the above chain, with or without posres and constraints turned on. Results: 1) Posres off, constraints off : step 0 WARNING: Listed nonbonded interaction between particles 1157 and 1163 == Why does it say particles and not atoms? Nevermind, its lysine on the surface of the protein, one of atoms is dimensionless hydrogen. (...) step 63: Water molecule starting at atom 7923 can not be settled. (...) Segmentation fault 2) Posres off, constraints on : Warning like above + LINCS warnings, all for charged aminoacids on surface of the protein Segfault at step 63 3) Posres on, constraints off, had to add refcoord_scaling = COM : WARNING: Listed nonbonded interaction between particles 3075 and 3079 == arginine on the surface, dimensionless hydrogen 4) Posres on, constraints on, refcoord_scaling = COM : Same warnings, several other positively charged dimensionless hydrogens listed, waters could not be settled, segfault. I tried to run few other peptides and proteins with tip5p, 100% of crashes. Also, tip5p has been used successfully with the charmm foce field: http://pubs.acs.org/doi/abs/10.1021/ct700053u Yes, there are no dimensionless charged hydrogens there except of these on ... tip3p, tip4p and tip5p water. (...) http://pubs.acs.org/doi/abs/10.1021/ct300180w (...) Are you using halogens with oplsaa-x? No, I use OPLSAA distributed with Gromacs. Standard oplsaa (non-x) and tip5p seem to be a fine combination: http://www.sciencedirect.com/science/article/pii/S0006349507713863 you might want to contact the authors of that paper to see if they ever had such problems. Thank you, I will ask them. I am starting to be sure, though, that it is not possible to run any simulations with tip5p and proteins (containing arginine for example) without some tricks, strengthening/constraining bonds at least. It happened during the minimization, that the distance between HHxy and NHx in arginine grew up to 1.48A, while HHxy was landing on LP of the water. Repeatability is 100%. Regards, Grzegorz Chris. Dear Chris, Thank you for your reply. I defined a new virtual atomtype (type D) with LJ sigma 1.72A ( 2*0.7+1.72=3.12, which is sigma of the oxygen) and played a bit with epsilon till the new LJ repulsion was able to prevent the build up of a huge force on the oxygen while interacting with dimensionless charged hydrogens. Also, I copied the flexibility parameters from tip4p to see if it helps in minimization before I turn it into rigid water - it seems that it does. I was able to minimize the system with such water. Also, I minimized the system with tip4p and replaced it with tip5p with a script. I tried to minimize the system afterwards with true tip5p, which did not work. My question is, besides the correctness of water model, why do you think it is safe to remove the LJ on lone electron pairs in MD? Will it not collapse like in energy minimization? Best Regards, Grzegorz -- 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] OPLS/AA + TIP5P, anybody?
Dear Chris, Thank you for your reply. I defined a new virtual atomtype (type D) with LJ sigma 1.72A ( 2*0.7+1.72=3.12, which is sigma of the oxygen) and played a bit with epsilon till the new LJ repulsion was able to prevent the build up of a huge force on the oxygen while interacting with dimensionless charged hydrogens. Also, I copied the flexibility parameters from tip4p to see if it helps in minimization before I turn it into rigid water - it seems that it does. I was able to minimize the system with such water. Also, I minimized the system with tip4p and replaced it with tip5p with a script. I tried to minimize the system afterwards with true tip5p, which did not work. My question is, besides the correctness of water model, why do you think it is safe to remove the LJ on lone electron pairs in MD? Will it not collapse like in energy minimization? Best Regards, Grzegorz On 2013-09-27 05:58, Christopher Neale wrote: Dear Gigo: I've never used tip5p, but perhaps you could add some LJ terms to the opls_120 definition, do your minimization, then remove the fake LJ term on opls_120 and run your MD? If that doesn't work, then you might be able to minimize your system using FLEXIBLE tip3p water and then use a script to convert the tip3p into tip5p. I expect that you can set 0,0,0 coordinates for each of the tip5p dummy atoms and that they will get correctly positioned in your first mdrun step with tip5p. Chris. -- original message -- Dear Mark, Thank you for your reply. Unfortunately, TIP5P is completely rigid and the FLEXIBLE define will not change it. Any other ideas? Best, g On 2013-09-24 23:51, Mark Abraham wrote: You should be able to minimize with CG and TIP5P by eliminating constraints, by making the water use a flexible molecule, e.g. define = -DFLEXIBLE (or something). Check your water .itp file for how to do it. 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] OPLS/AA + TIP5P, anybody?
Dear GMXers, Since I am interested in interactions of lone electron pairs of water oxygen within the active site of an enzyme that I work on, I decided to give TIP5P a shot. I use OPLSAA. I run into troubles very fast trying to minimize freshly solvated system. I found on the gmx-users (http://lists.gromacs.org/pipermail/gmx-users/2008-March/032732.html) that cg and constraints don't go together when TIP5P is to be used - thats OK. It turned out, however, that I was not able to minimize my protein even with steepest descent. The system minimizes with TIP4P pretty well (emtol=1.0). In the meantime I tried to minimize short peptide - 10aa, did not work as well. What happens? The LP of water used to get too close to positively charged hydrogens (without VDW radius) on arginine. It looks like this: Step= 579, Dmax= 8.0e-03 nm, Epot= -1.40714e+05 Fmax= 1.20925e+04, atom= 171 Step= 580, Dmax= 9.6e-03 nm, Epot= -1.41193e+05 Fmax= 8.13923e+04, atom= 171 Step= 581, Dmax= 1.1e-02 nm, Epot= -1.43034e+05 Fmax= 1.03648e+06, atom= 11181 Step= 585, Dmax= 1.7e-03 nm, Epot= -1.46878e+05 Fmax= 4.23958e+06, atom= 11181 Step= 587, Dmax= 1.0e-03 nm, Epot= -1.49565e+05 Fmax= 9.43285e+06, atom= 11181 Step= 589, Dmax= 6.2e-04 nm, Epot= -1.59042e+05 Fmax= 3.55920e+07, atom= 11181 Step= 591, Dmax= 3.7e-04 nm, Epot= -1.69054e+05 Fmax= 7.79944e+07, atom= 11181 Step= 593, Dmax= 2.2e-04 nm, Epot= -1.85575e+05 Fmax= 2.27640e+08, atom= 11181 Step= 595, Dmax= 1.3e-04 nm, Epot= -2.35034e+05 Fmax= 5.88938e+08, atom= 17181 Step= 597, Dmax= 8.0e-05 nm, Epot= -2.39154e+05 Fmax= 1.22615e+09, atom= 11181 Step= 598, Dmax= 9.6e-05 nm, Epot= -2.67157e+05 Fmax= 1.96782e+09, atom= 11181 Step= 600, Dmax= 5.8e-05 nm, Epot= -4.37260e+05 Fmax= 1.08988e+10, atom= 11181 Step= 602, Dmax= 3.5e-05 nm, Epot= -4.65654e+05 Fmax= 1.29609e+10, atom= 11181 Step= 604, Dmax= 2.1e-05 nm, Epot= -1.17945e+06 Fmax= 1.31028e+11, atom= 11181 Step= 607, Dmax= 6.3e-06 nm, Epot= -3.07551e+06 Fmax= 6.04297e+11, atom= 11181 Step= 610, Dmax= 1.9e-06 nm, Epot= -4.26709e+06 Fmax= 1.61390e+12, atom= 11181 Step= 611, Dmax= 2.3e-06 nm, Epot= -4.39724e+06 Fmax= 2.14416e+12, atom= 11181 Step= 613, Dmax= 1.4e-06 nm, Epot= -1.27489e+07 Fmax= 1.03223e+13, atom= 17181 Step= 614, Dmax= 1.6e-06 nm, Epot= -5.23118e+06 Fmax= 3.18465e+12, atom= 11181 Energy minimization has stopped, but the forces havenot converged to the (...) In this example atom 171 is HH21 of ARG, and 11181 is oxygen of water that got close to this ARG. Sometimes the epot turns nan at the end. If you would like to reproduce, I put the peptide.pdb, the mdp file and the running script at http://shroom.ibb.waw.pl/tip5p . If anybody have any suggestions how to minimize (deep) with OPLSAA + TIP5P in gromacs (4.6.3 preferably...) without constraining bond lengths (which is also problematic), I will be very very grateful. Best, Grzegorz Wieczorek -- 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] OPLS/AA + TIP5P, anybody?
Dear Mark, Thank you for your reply. Unfortunately, TIP5P is completely rigid and the FLEXIBLE define will not change it. Any other ideas? Best, g On 2013-09-24 23:51, Mark Abraham wrote: You should be able to minimize with CG and TIP5P by eliminating constraints, by making the water use a flexible molecule, e.g. define = -DFLEXIBLE (or something). Check your water .itp file for how to do it. Mark On Tue, Sep 24, 2013 at 10:25 PM, gigo g...@ibb.waw.pl wrote: Dear GMXers, Since I am interested in interactions of lone electron pairs of water oxygen within the active site of an enzyme that I work on, I decided to give TIP5P a shot. I use OPLSAA. I run into troubles very fast trying to minimize freshly solvated system. I found on the gmx-users (http://lists.gromacs.org/pipermail/gmx-users/2008-March/032732.html) that cg and constraints don't go together when TIP5P is to be used - thats OK. It turned out, however, that I was not able to minimize my protein even with steepest descent. The system minimizes with TIP4P pretty well (emtol=1.0). In the meantime I tried to minimize short peptide - 10aa, did not work as well. What happens? The LP of water used to get too close to positively charged hydrogens (without VDW radius) on arginine. It looks like this: Step= 579, Dmax= 8.0e-03 nm, Epot= -1.40714e+05 Fmax= 1.20925e+04, atom= 171 Step= 580, Dmax= 9.6e-03 nm, Epot= -1.41193e+05 Fmax= 8.13923e+04, atom= 171 Step= 581, Dmax= 1.1e-02 nm, Epot= -1.43034e+05 Fmax= 1.03648e+06, atom= 11181 Step= 585, Dmax= 1.7e-03 nm, Epot= -1.46878e+05 Fmax= 4.23958e+06, atom= 11181 Step= 587, Dmax= 1.0e-03 nm, Epot= -1.49565e+05 Fmax= 9.43285e+06, atom= 11181 Step= 589, Dmax= 6.2e-04 nm, Epot= -1.59042e+05 Fmax= 3.55920e+07, atom= 11181 Step= 591, Dmax= 3.7e-04 nm, Epot= -1.69054e+05 Fmax= 7.79944e+07, atom= 11181 Step= 593, Dmax= 2.2e-04 nm, Epot= -1.85575e+05 Fmax= 2.27640e+08, atom= 11181 Step= 595, Dmax= 1.3e-04 nm, Epot= -2.35034e+05 Fmax= 5.88938e+08, atom= 17181 Step= 597, Dmax= 8.0e-05 nm, Epot= -2.39154e+05 Fmax= 1.22615e+09, atom= 11181 Step= 598, Dmax= 9.6e-05 nm, Epot= -2.67157e+05 Fmax= 1.96782e+09, atom= 11181 Step= 600, Dmax= 5.8e-05 nm, Epot= -4.37260e+05 Fmax= 1.08988e+10, atom= 11181 Step= 602, Dmax= 3.5e-05 nm, Epot= -4.65654e+05 Fmax= 1.29609e+10, atom= 11181 Step= 604, Dmax= 2.1e-05 nm, Epot= -1.17945e+06 Fmax= 1.31028e+11, atom= 11181 Step= 607, Dmax= 6.3e-06 nm, Epot= -3.07551e+06 Fmax= 6.04297e+11, atom= 11181 Step= 610, Dmax= 1.9e-06 nm, Epot= -4.26709e+06 Fmax= 1.61390e+12, atom= 11181 Step= 611, Dmax= 2.3e-06 nm, Epot= -4.39724e+06 Fmax= 2.14416e+12, atom= 11181 Step= 613, Dmax= 1.4e-06 nm, Epot= -1.27489e+07 Fmax= 1.03223e+13, atom= 17181 Step= 614, Dmax= 1.6e-06 nm, Epot= -5.23118e+06 Fmax= 3.18465e+12, atom= 11181 Energy minimization has stopped, but the forces havenot converged to the (...) In this example atom 171 is HH21 of ARG, and 11181 is oxygen of water that got close to this ARG. Sometimes the epot turns nan at the end. If you would like to reproduce, I put the peptide.pdb, the mdp file and the running script at http://shroom.ibb.waw.pl/tip5p . If anybody have any suggestions how to minimize (deep) with OPLSAA + TIP5P in gromacs (4.6.3 preferably...) without constraining bond lengths (which is also problematic), I will be very very grateful. Best, Grzegorz Wieczorek -- 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] Problems with REMD in Gromacs 4.6.3
Hi! On 2013-07-17 21:08, Mark Abraham wrote: You tried ppn3 (with and without --loadbalance)? I was testing on 8-replicas simulation. 1) Without --loadbalance and -np 8. Excerpts from the script: #PBS -l nodes=8:ppn=3 setenv OMP_NUM_THREADS 4 mpiexec mdrun_mpi -v -cpt 20 -multi 8 -ntomp 4 -replex 2500 -cpi -pin on Excerpts from logs: Using 3 MPI processes Using 4 OpenMP threads per MPI process (...) Overriding thread affinity set outside mdrun_mpi Pinning threads with an auto-selected logical core stride of 1 WARNING: In MPI process #0: Affinity setting for 1/4 threads failed. This can cause performance degradation! If you think your setting are correct, contact the GROMACS developers. WARNING: In MPI process #2: Affinity setting for 4/4 threads failed. Load: The job was allocated 24 cores (3 cores on 8 different nodes). Each OpenMP thread uses ~1/3 of a CPU core on average. Conclusions: MPI runs as many processes as cores requested (nnodes*ppn=24), it ignores OMP_NUM_THREADS env == this is wrong and is not Gromacs issue. Each MPI process forks to 4 threads as requested. The 24-core limit granted by Torque is not violated. 2) The same script, but with -np 8, to limit the number of MPI processes to the number of replicas Logs: Using 1 MPI process Using 4 OpenMP threads (...) Replicas 0,3 and 6: WARNING: Affinity setting for 1/4 threads failed. Replicas 1,2,4,5,7: WARNING: Affinity setting for 4/4 threads failed. Load: The job was allocated 24 cores on 8 nodes. Only on first 3 nodes mpiexec was run. Each OpenMP thread uses ~20% of a CPU core. 3) -np 8 --loadbalance Excerpts from logs: Using 1 MPI process Using 4 OpenMP threads (...) Each replica says: WARNING: Affinity setting for 3/4 threads failed. Load: MPI processes spread evenly on all 8 nodes. Each OpenMP thread uses ~50% of a CPU core. 4) -np 8 --loadbalance, #PBS -l nodes=8:ppn=4 == this worked ~OK with gromacs 4.6.2 Logs: WARNING: Affinity setting for 2/4 threads failed. Load: 32 cores allocated on 8 nodes. MPI processes spread evenly, each OpenMP thread uses ~70% of a CPU core. With 144 replicas the simulation did not produce any results, just got stuck. Some thoughts: the main problem is most probably in the way MPI interprets the information from torque, it is not Gromacs related. MPI ignores OMP_NUM_THREADS. The environment is just broken. Since gromacs-4.6.2 behaved better than 4.6.3 there, I am coming back to it. Best, G Mark On Wed, Jul 17, 2013 at 6:30 PM, gigo g...@ibb.waw.pl wrote: On 2013-07-13 11:10, Mark Abraham wrote: On Sat, Jul 13, 2013 at 1:24 AM, gigo g...@ibb.waw.pl wrote: On 2013-07-12 20:00, Mark Abraham wrote: On Fri, Jul 12, 2013 at 4:27 PM, gigo g...@ibb.waw.pl wrote: Hi! On 2013-07-12 11:15, Mark Abraham wrote: What does --loadbalance do? It balances the total number of processes across all allocated nodes. OK, but using it means you are hostage to its assumptions about balance. Thats true, but as long as I do not try to use more resources that the torque gives me, everything is OK. The question is, what is a proper way of running multiple simulations in parallel with MPI that are further parallelized with OpenMP, when pinning fails? I could not find any other. I think pinning fails because you are double-crossing yourself. You do not want 12 MPI processes per node, and that is likely what ppn is setting. AFAIK your setup should work, but I haven't tested it. The thing is that mpiexec does not know that I want each replica to fork to 4 OpenMP threads. Thus, without this option and without affinities (in a sec about it) mpiexec starts too many replicas on some nodes - gromacs complains about the overload then - while some cores on other nodes are not used. It is possible to run my simulation like that: mpiexec mdrun_mpi -v -cpt 20 -multi 144 -replex 2000 -cpi (without --loadbalance for mpiexec and without -ntomp for mdrun) Then each replica runs on 4 MPI processes (I allocate 4 times more cores then replicas and mdrun sees it). The problem is that it is much slower than using OpenMP for each replica. I did not find any other way than --loadbalance in mpiexec and then -multi 144 -ntomp 4 in mdrun to use MPI and OpenMP at the same time on the torque-controlled cluster. That seems highly surprising. I have not yet encountered a job scheduler that was completely lacking a do what I tell you layout scheme. More importantly, why are you using #PBS -l nodes=48:ppn=12? I thing that torque is very similar to all PBS-like resource managers in this regard. It actually does what I tell it to do. There are 12-core nodes, I ask for 48 of them - I get them (simple #PBS -l ncpus=576 does not work), end of story. Now, the program that I run is responsible for populating resources that I got. No, that's not the end of the story. The scheduler and the MPI system typically cooperate to populate
Re: [gmx-users] Problems with REMD in Gromacs 4.6.3
On 2013-07-13 11:10, Mark Abraham wrote: On Sat, Jul 13, 2013 at 1:24 AM, gigo g...@ibb.waw.pl wrote: On 2013-07-12 20:00, Mark Abraham wrote: On Fri, Jul 12, 2013 at 4:27 PM, gigo g...@ibb.waw.pl wrote: Hi! On 2013-07-12 11:15, Mark Abraham wrote: What does --loadbalance do? It balances the total number of processes across all allocated nodes. OK, but using it means you are hostage to its assumptions about balance. Thats true, but as long as I do not try to use more resources that the torque gives me, everything is OK. The question is, what is a proper way of running multiple simulations in parallel with MPI that are further parallelized with OpenMP, when pinning fails? I could not find any other. I think pinning fails because you are double-crossing yourself. You do not want 12 MPI processes per node, and that is likely what ppn is setting. AFAIK your setup should work, but I haven't tested it. The thing is that mpiexec does not know that I want each replica to fork to 4 OpenMP threads. Thus, without this option and without affinities (in a sec about it) mpiexec starts too many replicas on some nodes - gromacs complains about the overload then - while some cores on other nodes are not used. It is possible to run my simulation like that: mpiexec mdrun_mpi -v -cpt 20 -multi 144 -replex 2000 -cpi (without --loadbalance for mpiexec and without -ntomp for mdrun) Then each replica runs on 4 MPI processes (I allocate 4 times more cores then replicas and mdrun sees it). The problem is that it is much slower than using OpenMP for each replica. I did not find any other way than --loadbalance in mpiexec and then -multi 144 -ntomp 4 in mdrun to use MPI and OpenMP at the same time on the torque-controlled cluster. That seems highly surprising. I have not yet encountered a job scheduler that was completely lacking a do what I tell you layout scheme. More importantly, why are you using #PBS -l nodes=48:ppn=12? I thing that torque is very similar to all PBS-like resource managers in this regard. It actually does what I tell it to do. There are 12-core nodes, I ask for 48 of them - I get them (simple #PBS -l ncpus=576 does not work), end of story. Now, the program that I run is responsible for populating resources that I got. No, that's not the end of the story. The scheduler and the MPI system typically cooperate to populate the MPI processes on the hardware, set OMP_NUM_THREADS, set affinities, etc. mdrun honours those if they are set. I was able to run what I wanted flawlessly on another cluster with PBS-Pro. The torque cluster seem to work like I said (the end of story behaviour). REMD runs well on torque when I give a whole physical node to one replica. Otherwise the simulation does not go or the pinning fails (sometimes partially). I run out of options, I did not find any working example/documentation on running hybrid MPI/OpenMP jobs in torque. It seems that I stumbled upon limitations of this resource manager, and it is not really the Gromacs issue. Best Regards, Grzegorz You seem to be using 12 because you know there are 12 cores per node. The scheduler should know that already. ppn should be a command about what to do with the hardware, not a description of what it is. More to the point, you should read the docs and be sure what it does. Surely you want 3 MPI processes per 12-core node? Yes - I want each node to run 3 MPI processes. Preferably, I would like to run each MPI process on separate node (spread on 12 cores with OpenMP) but I will not get as much of resources. But again, without the --loadbalance hack I would not be able to properly populate the nodes... So try ppn 3! What do the .log files say about OMP_NUM_THREADS, thread affinities, pinning, etc? Each replica logs: Using 1 MPI process Using 4 OpenMP threads, That is is correct. As I said, the threads are forked, but 3 out of 4 don't do anything, and the simulation does not go at all. About affinities Gromacs says: Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. Well, the current platform is normal x86_64 cluster, but the whole information about resources is passed by Torque to OpenMPI-linked Gromacs. Can it be that mdrun sees the resources allocated by torque as a big pool of cpus and misses the information about nodes topology? mdrun gets its processor topology from the MPI layer, so that is where you need to focus. The error message confirms that GROMACS sees things that seem wrong. Thank you, I will take a look. But the first thing I want to do is finding the reason why Gromacs 4.6.3 is not able to run on my (slightly weird, I admit) setup, while 4.6.2 does it very well. 4.6.2 had a bug that inhibited any MPI-based mdrun from attempting to set affinities. It's still not clear
Re: [gmx-users] Problems with REMD in Gromacs 4.6.3
Hi! On 2013-07-12 11:15, Mark Abraham wrote: What does --loadbalance do? It balances the total number of processes across all allocated nodes. The thing is that mpiexec does not know that I want each replica to fork to 4 OpenMP threads. Thus, without this option and without affinities (in a sec about it) mpiexec starts too many replicas on some nodes - gromacs complains about the overload then - while some cores on other nodes are not used. It is possible to run my simulation like that: mpiexec mdrun_mpi -v -cpt 20 -multi 144 -replex 2000 -cpi (without --loadbalance for mpiexec and without -ntomp for mdrun) Then each replica runs on 4 MPI processes (I allocate 4 times more cores then replicas and mdrun sees it). The problem is that it is much slower than using OpenMP for each replica. I did not find any other way than --loadbalance in mpiexec and then -multi 144 -ntomp 4 in mdrun to use MPI and OpenMP at the same time on the torque-controlled cluster. What do the .log files say about OMP_NUM_THREADS, thread affinities, pinning, etc? Each replica logs: Using 1 MPI process Using 4 OpenMP threads, That is is correct. As I said, the threads are forked, but 3 out of 4 don't do anything, and the simulation does not go at all. About affinities Gromacs says: Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. Well, the current platform is normal x86_64 cluster, but the whole information about resources is passed by Torque to OpenMPI-linked Gromacs. Can it be that mdrun sees the resources allocated by torque as a big pool of cpus and misses the information about nodes topology? If you have any suggestions how to debug or trace this issue, I would be glad to participate. Best, G Mark On Fri, Jul 12, 2013 at 3:46 AM, gigo g...@poczta.ibb.waw.pl wrote: Dear GMXers, With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4 cores with OpenMP. There is Torque installed on the cluster build of 12-cores nodes, so I used the following script: #!/bin/tcsh -f #PBS -S /bin/tcsh #PBS -N test #PBS -l nodes=48:ppn=12 #PBS -l walltime=300:00:00 #PBS -l mem=288Gb #PBS -r n cd $PBS_O_WORKDIR mpiexec -np 144 --loadbalance mdrun_mpi -v -cpt 20 -multi 144 -ntomp 4 -replex 2000 It was working just great with 4.6.2. It does not work with 4.6.3. The new version was compiled with the same options in the same environment. Mpiexec spreads the replicas evenly over the cluster. Each replica forks 4 threads, but only one of them uses any cpu. Logs end at the citations. Some empty energy and trajectory files are created, nothing is written to them. Please let me know if you have any immediate suggestion on how to make it work (maybe based on some differences between versions), or if I should fill the bug report with all the technical details. Best Regards, Grzegorz Wieczorek -- 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] remd
Hi! On 2013-07-12 07:58, Shine A wrote: Hi Sir, Is it possible to run an REMD simulation having 16 replicas in a cluster(group of cpu) having 8 nodes. Here each node have 8 processors. It is possible. If you have Gromacs (version = 4.6) compiled with MPI and you specify the number of replicas (-multi 16) in the mdrun command and 64 processors are allocated by mpirun, mdrun should start 4 MPI processes per each replica. It worked for me, at least. With OpenMP parallelization it would run faster, I have some problems with it though. Read the latest posts Problems with REMD in Gromacs 4.6.3. Best, G -- 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] Problems with REMD in Gromacs 4.6.3
On 2013-07-12 20:00, Mark Abraham wrote: On Fri, Jul 12, 2013 at 4:27 PM, gigo g...@ibb.waw.pl wrote: Hi! On 2013-07-12 11:15, Mark Abraham wrote: What does --loadbalance do? It balances the total number of processes across all allocated nodes. OK, but using it means you are hostage to its assumptions about balance. Thats true, but as long as I do not try to use more resources that the torque gives me, everything is OK. The question is, what is a proper way of running multiple simulations in parallel with MPI that are further parallelized with OpenMP, when pinning fails? I could not find any other. The thing is that mpiexec does not know that I want each replica to fork to 4 OpenMP threads. Thus, without this option and without affinities (in a sec about it) mpiexec starts too many replicas on some nodes - gromacs complains about the overload then - while some cores on other nodes are not used. It is possible to run my simulation like that: mpiexec mdrun_mpi -v -cpt 20 -multi 144 -replex 2000 -cpi (without --loadbalance for mpiexec and without -ntomp for mdrun) Then each replica runs on 4 MPI processes (I allocate 4 times more cores then replicas and mdrun sees it). The problem is that it is much slower than using OpenMP for each replica. I did not find any other way than --loadbalance in mpiexec and then -multi 144 -ntomp 4 in mdrun to use MPI and OpenMP at the same time on the torque-controlled cluster. That seems highly surprising. I have not yet encountered a job scheduler that was completely lacking a do what I tell you layout scheme. More importantly, why are you using #PBS -l nodes=48:ppn=12? I thing that torque is very similar to all PBS-like resource managers in this regard. It actually does what I tell it to do. There are 12-core nodes, I ask for 48 of them - I get them (simple #PBS -l ncpus=576 does not work), end of story. Now, the program that I run is responsible for populating resources that I got. Surely you want 3 MPI processes per 12-core node? Yes - I want each node to run 3 MPI processes. Preferably, I would like to run each MPI process on separate node (spread on 12 cores with OpenMP) but I will not get as much of resources. But again, without the --loadbalance hack I would not be able to properly populate the nodes... What do the .log files say about OMP_NUM_THREADS, thread affinities, pinning, etc? Each replica logs: Using 1 MPI process Using 4 OpenMP threads, That is is correct. As I said, the threads are forked, but 3 out of 4 don't do anything, and the simulation does not go at all. About affinities Gromacs says: Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. Well, the current platform is normal x86_64 cluster, but the whole information about resources is passed by Torque to OpenMPI-linked Gromacs. Can it be that mdrun sees the resources allocated by torque as a big pool of cpus and misses the information about nodes topology? mdrun gets its processor topology from the MPI layer, so that is where you need to focus. The error message confirms that GROMACS sees things that seem wrong. Thank you, I will take a look. But the first thing I want to do is finding the reason why Gromacs 4.6.3 is not able to run on my (slightly weird, I admit) setup, while 4.6.2 does it very well. Best, Grzegorz -- 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] Problems with REMD in Gromacs 4.6.3
Dear GMXers, With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4 cores with OpenMP. There is Torque installed on the cluster build of 12-cores nodes, so I used the following script: #!/bin/tcsh -f #PBS -S /bin/tcsh #PBS -N test #PBS -l nodes=48:ppn=12 #PBS -l walltime=300:00:00 #PBS -l mem=288Gb #PBS -r n cd $PBS_O_WORKDIR mpiexec -np 144 --loadbalance mdrun_mpi -v -cpt 20 -multi 144 -ntomp 4 -replex 2000 It was working just great with 4.6.2. It does not work with 4.6.3. The new version was compiled with the same options in the same environment. Mpiexec spreads the replicas evenly over the cluster. Each replica forks 4 threads, but only one of them uses any cpu. Logs end at the citations. Some empty energy and trajectory files are created, nothing is written to them. Please let me know if you have any immediate suggestion on how to make it work (maybe based on some differences between versions), or if I should fill the bug report with all the technical details. Best Regards, Grzegorz Wieczorek -- 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] Problems with REMD in Gromacs 4.6.3
Dear GMXers, With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4 cores with OpenMP. There is Torque installed on the cluster build of 12-cores nodes, so I used the following script: #!/bin/tcsh -f #PBS -S /bin/tcsh #PBS -N test #PBS -l nodes=48:ppn=12 #PBS -l walltime=300:00:00 #PBS -l mem=288Gb #PBS -r n cd $PBS_O_WORKDIR mpiexec -np 144 --loadbalance mdrun_mpi -v -cpt 20 -multi 144 -ntomp 4 -replex 2000 It was working just great with 4.6.2. It does not work with 4.6.3. The new version was compiled with the same options in the same environment. Mpiexec spreads the replicas evenly over the cluster. Each replica forks 4 threads, but only one of them uses any cpu. Logs end at the citations. Some empty energy and trajectory files are created, nothing is written to them. Please let me know if you have any immediate suggestion on how to make it work (maybe based on some differences between versions), or if I should fill the bug report with all the technical details. Best Regards, Grzegorz Wieczorek Ps. I'm sending this message for the 3rd time - it did not appear on the list the last 2 times. Just in case - sorry for the spam. -- 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] Problem with running REMD in Gromacs 4.6.3
Dear GMXers, With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4 cores with OpenMP. There is Torque installed on the cluster build of 12-cores nodes, so I used the following script: #!/bin/tcsh -f #PBS -S /bin/tcsh #PBS -N test #PBS -l nodes=48:ppn=12 #PBS -l walltime=300:00:00 #PBS -l mem=288Gb #PBS -r n cd $PBS_O_WORKDIR mpiexec -np 144 --loadbalance mdrun_mpi -v -cpt 20 -multi 144 -ntomp 4 -replex 2000 It was working just great with 4.6.2. It does not work with 4.6.3. The new version was compiled with the same options in the same environment. Mpiexec spreads the replicas evenly over the cluster. Each replica forks 4 threads, but only one of them uses any cpu. Logs end at the citations. Some empty energy and trajectory files are created, nothing is written to them. Please let me know if you have any immediate suggestion on how to make it work (maybe based on some differences between versions), or if I should fill the bug report with all the technical details. Best Regards, Grzegorz Wieczorek -- 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] Nucleic Acid Simulations with Gromacs
Hi, On the gromacs webpage in user contributions-topologies you have (at least) 2 forcefields do download that allow you to simulate NA. The first is OPLS NA records from rnp-group (http://rnp-group.genebee.msu.su/3d/oplsa_ff.html). It is for gromacs 3.2.1, so minor manual adjustments for 3.3.1 are required. The second is AMBER ff variants from Stanford (http://folding.stanford.edu/ffamber/). Good Luck Grzegorz Wieczorek Department of Bioinformatics Institute of Biochemistry and Biophysics Polish Academy of Sciences ul. Pawinskiego 5a 02-106 Warszawa, Poland On Tue, 2 Oct 2007, Monika Sharma wrote: Dear All, I want to start nucleic acid simulations. I am using gromacs3.3.1. But I could not find any mention of Nucleic Acids in any of the force-field provided by gromacs distro. So does it mean that one _can not_ simulate nucleic acids with gromacs. Has anyone tried? And if someone can guide me through?? Thanks in advance Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] openmpi
Hi, I'm using openmpi on our 24-nodes 2 cores each cluster without any problem so far. I run my jobs under torque and I did not change any of default settings. With my system it scales rather well on 4 nodes, but I have no problems with running more. Grzegorz Wieczorek Department of Bioinformatics Institute of Biochemistry and Biophysics Polish Academy of Sciences ul. Pawinskiego 5a 02-106 Warszawa, Poland On Thu, 14 Sep 2006, [EMAIL PROTECTED] wrote: Anyone using openmpi for parallel gromacs? If so, how to set the maximum short tcp length? I have tried some things unsuccessfully which are posted at the open mpi site: http://www.open-mpi.org/community/lists/users/2006/09/1864.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
