[gmx-users] (no subject)
Dear GMX Users, I am wish to perform a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a open-state, the system moves to the closed-state and just stays there forever (20 ns) simulation. I use the following command. make_edi -f eigenvec.trr -eig eigenval.xvg -s 1pdb.pdb -o sam.edi -flood 7-16 -tau 0 -Eflnull 450.0 -hessian -alpha 2 -ori 1pdb.pdb -T 50 the eigenvec.trr was generated from anisotropic network models. How should I organize the different parameters to effect this transition. As of now I am executing my commands (and also my understanding) are based on the following paper: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20473/abstract Best, nahren -- 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] Conformational transition using essential dynamics
Dear GMX Users, I am wish to perform a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a open-state, the system moves to the closed-state and just stays there forever (20 ns) simulation. I use the following command. make_edi -f eigenvec.trr -eig eigenval.xvg -s 1pdb.pdb -o sam.edi -flood 7-16 -tau 0 -Eflnull 450.0 -hessian -alpha 2 -ori 1pdb.pdb -T 50 the eigenvec.trr was generated from anisotropic network models. How should I organize the different parameters to effect this transition. As of now I am executing my commands (and also my understanding) are based on the following paper: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20473/abstract Best, nahren -- 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] g_lie and ligand only simulation
Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME? Thank you Regards Kavya On Wed, Nov 6, 2013 at 11:52 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, When the simulation was carried out with PME rcoulomb was set equal to rlist. But when I need to to ligand-water simulation without PME (with RF-0) then it requires rlist greater by 0.1-0.3 than rcoulomb. So if I rerun protein-ligand-water simulation there could be more differences in the energies isnt it? Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:51 PM, Kavyashree M hmkv...@gmail.com wrote: Ok thank you. I thought it was for protein-ligand-water that needs to be rerun without PME. Thanks Regards Kavya On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 12:14 PM, Kavyashree M wrote: Sir, Thank you. Should the ligand-water MD be done without PME? I already answered this. Please read my previous reply again. -Justin Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -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 -- == 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 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: Gromacs-4.6 on two Titans GPUs
Hi Dwey, On 05/11/13 22:00, Dwey Kauffman wrote: Hi Szilard, Thanks for your suggestions. I am indeed aware of this page. In a 8-core AMD with 1GPU, I am very happy about its performance. See below. My intention is to obtain a even better one because we have multiple nodes. ### 8 core AMD with 1 GPU, Force evaluation time GPU/CPU: 4.006 ms/2.578 ms = 1.554 For optimal performance this ratio should be close to 1! NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. Core t (s) Wall t (s)(%) Time: 216205.51027036.812 799.7 7h30:36 (ns/day)(hour/ns) Performance: 31.9560.751 ### 8 core AMD with 2 GPUs Core t (s) Wall t (s)(%) Time: 178961.45022398.880 799.0 6h13:18 (ns/day)(hour/ns) Performance: 38.5730.622 Finished mdrun on node 0 Sat Jul 13 09:24:39 2013 I'm almost certain that Szilard meant the lines above this that give the breakdown of where the time is spent in the simulation. Richard However, in your case I suspect that the bottleneck is multi-threaded scaling on the AMD CPUs and you should probably decrease the number of threads per MPI rank and share GPUs between 2-4 ranks. OK but can you give a example of mdrun command ? given a 8 core AMD with 2 GPUs. I will try to run it again. Regarding scaling across nodes, you can't expect much from gigabit ethernet - especially not from the cheaper cards/switches, in my experience even reaction field runs don't scale across nodes with 10G ethernet if you have more than 4-6 ranks per node trying to communicate (let alone with PME). However, on infiniband clusters we have seen scaling to 100 atoms/core (at peak). From your comments, it sounds like a cluster of AMD cpus is difficult to scale across nodes in our current setup. Let's assume we install Infiniband (20 or 40GB/s) in the same system of 16 nodes of 8 core AMD with 1 GPU only. Considering the same AMD system, what is a good way to obtain better performance when we run a task across nodes ? in other words, what dose mudrun_mpi look like ? Thanks, Dwey -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-4-6-on-two-Titans-GPUs-tp5012186p5012279.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] Re: Analysis tools and triclinic boxes
On 11/5/13 7:14 PM, Stephanie Teich-McGoldrick wrote: Message: 5 Date: Mon, 04 Nov 2013 13:32:52 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Analysis tools and triclinic boxes To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5277e854.9000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Justin, Thanks for the response. My question was prompted by line 243 in gmx_cluster.c which states /* Should use pbc_dx when analysing multiple molecueles,but the box is not stored for every frame.*/ I just wanted to verify that analysis tools are written for any box shape. I have never had any problems with any of the analysis tools using any of the box shapes, though that of course does not negate the possibility of problems. The comments in pbc.h describe all of the functions quite well and what the potential issues might be. If there is a demonstrable problem with something, that is certainly worth pursuing. -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] g_lie and ligand only simulation
On 11/6/13 5:47 AM, Kavyashree M wrote: Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME? The energies are inherently going to be different because you are evaluating nonbonded energies with different methods. Typically, I think people just use long cutoffs for the recalculation. -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] g_lie and ligand only simulation
Thank you.. On Wed, Nov 6, 2013 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/6/13 5:47 AM, Kavyashree M wrote: Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME? The energies are inherently going to be different because you are evaluating nonbonded energies with different methods. Typically, I think people just use long cutoffs for the recalculation. -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 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] Number of water molecules around any methyl carbon
Hi all, I would like to calculate the number of water molecules around any of the methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an index group containing all three of the methyl carbon atoms and used trjorder -nshell to calculate the number of oxygen atoms within a specified cutoff distance of this index group. What I am trying to figure out is whether this method results in the number of oxygen atoms around any single methyl carbon or all methyl carbon atoms. Does anyone have any insights regarding this problem? If the described method does not calculate the number of oxygen atoms around all of the methyl carbon atoms, is there a way to do so, without overcounting? Thanks, Blake PhD Candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/Number-of-water-molecules-around-any-methyl-carbon-tp5012297.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
[gmx-users] Enterobactin binding to Iron(III)
I was told before I would need to use quantum calculations to do this. What software and method would you suggest to do this? Thanks. -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] stopped simulation
Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough? I appreciate any help/suggestion regarding my case. Kind regards, Ehsan -- 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] Group protein not found in indexfile
Hello I am having trouble running a dimmer invacuo simulation. I can do energy minimization on it, but when I attempt to generate md.tpr file I get this weird message about “Group Protein not found in index”. I don’t see why I would need an index file. I have no trouble generating a md.tpr file for md (afer energy minimization) IF I solvate the system. It is only in a vacuum that I cannot generate a .tpr file using grompp. Has anyone else had this symptom with Gromacs? I have worked on this a couple of days and would appreciate any help… Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Number of water molecules around any methyl carbon
On 11/6/13 10:55 AM, rankinb wrote: Hi all, I would like to calculate the number of water molecules around any of the methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an index group containing all three of the methyl carbon atoms and used trjorder -nshell to calculate the number of oxygen atoms within a specified cutoff distance of this index group. What I am trying to figure out is whether this method results in the number of oxygen atoms around any single methyl carbon or all methyl carbon atoms. Does anyone have any insights regarding this problem? If the described method does not calculate the number of oxygen atoms around all of the methyl carbon atoms, is there a way to do so, without overcounting? It should account for all of the methyl groups simultaneously, but you'd have to go into the code to see if it is doing the searching based on all of the atoms or just the group's center of mass. In the latter case, you'd be potentially under-counting the number of waters. Integrating an RDF would be a more conventional approach. -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] stopped simulation
On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough? I appreciate any help/suggestion regarding my case. The cutoffs values (1.5) are wrong for using any of the Gromos parameter sets. Likely the dynamics have become unstable due to violation of the physical model. -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] Group protein not found in indexfile
On 11/6/13 1:52 PM, Steve Seibold wrote: Hello I am having trouble running a dimmer invacuo simulation. I can do energy minimization on it, but when I attempt to generate md.tpr file I get this weird message about “Group Protein not found in index”. I don’t see why I would need an index file. I have no trouble generating a md.tpr file for md (afer energy minimization) IF I solvate the system. It is only in a vacuum that I cannot generate a .tpr file using grompp. Has anyone else had this symptom with Gromacs? I was trying to help you before: http://lists.gromacs.org/pipermail/gmx-users/2013-November/085179.html but the thread went cold, so I assumed you had fixed it. If you're still having problems, we still need to see the information I asked for before. -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] stopped simulation
Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough? I appreciate any help/suggestion regarding my case. The cutoffs values (1.5) are wrong for using any of the Gromos parameter sets. Likely the dynamics have become unstable due to violation of the physical model. -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! *
Re: [gmx-users] stopped simulation
On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough? I appreciate any help/suggestion regarding my case. The cutoffs values (1.5) are wrong for using any of the Gromos parameter sets. Likely the dynamics have become unstable due to violation of the physical model. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences
Re: [gmx-users] stopped simulation
What is this cut-off radius mentioned in the manual? The cut-off radius used to truncate non-bonded inter-actions may not exceed half the shortest box vector. Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 11:22:09 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs
Re: [gmx-users] stopped simulation
On 11/6/13 2:27 PM, Ehsan Sadeghi wrote: What is this cut-off radius mentioned in the manual? The cut-off radius used to truncate non-bonded inter-actions may not exceed half the shortest box vector. It refers to the longest cutoff used to evaluate nonbonded interactions, whatever that may be for your chosen force field. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 11:22:09 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320
Re: [gmx-users] Number of water molecules around any methyl carbon
Count the number of O observed near each C singly and compare the four numbers. Mark On Nov 6, 2013 4:57 PM, rankinb rank...@purdue.edu wrote: Hi all, I would like to calculate the number of water molecules around any of the methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an index group containing all three of the methyl carbon atoms and used trjorder -nshell to calculate the number of oxygen atoms within a specified cutoff distance of this index group. What I am trying to figure out is whether this method results in the number of oxygen atoms around any single methyl carbon or all methyl carbon atoms. Does anyone have any insights regarding this problem? If the described method does not calculate the number of oxygen atoms around all of the methyl carbon atoms, is there a way to do so, without overcounting? Thanks, Blake PhD Candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/Number-of-water-molecules-around-any-methyl-carbon-tp5012297.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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About g_potential
Dear Justin and all the colleagues, I am just trying to use g_potential to do the analysis of model. However, one thing puzzled me is about the slice number -sl. When different slice numbers are defined, the calculated potential is also different. I do not know the reason of that. Could you please give me a clue to that, and also which slide number would provide more accurate results? Thanks very much! Best wishes, Guangwei Jiang -- 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] Analysis tools and triclinic boxes
Hi, They ought to, and we hope they do, but historically quality control of analysis tools was threadbare, there is no testing of that kind of thing now, and certainly no implied warranty. Especially at the existing price point! ;-) That comment could easily refer to (or be) an archaic code version, I'm afraid. If you have doubts, please try to verify with a simple system the behaviour you expect. Mark On Mon, Nov 4, 2013 at 7:29 PM, Stephanie Teich-McGoldrick stephani...@gmail.com wrote: Dear all, I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail list, it is my understanding that the default box shape in gromacs in a triclinic box. Can I assume that all the analysis tools also work for a triclinic box. Cheers, Stephanie -- 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] stopped simulation
On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Triple counting is not possible, per minimum-image convention. I think Ehsan's report of a 0.5nm box size is probably wrong, e.g. per its documentation, editconf -d 0.5 does not produce a 0.5nm box. Mark Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long
Re: [gmx-users] stopped simulation
On 11/6/13 4:52 PM, Mark Abraham wrote: On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Triple counting is not possible, per minimum-image convention. I think True. Thinking too quickly ;) Ehsan's report of a 0.5nm box size is probably wrong, e.g. per its documentation, editconf -d 0.5 does not produce a 0.5nm box. editconf -box 0.5 does produce such a box, though, so it is possible. grompp should have warned quite obviously about the combination of a 0.5-nm box with 1.5-nm cutoffs, though. -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: single point calculation with gromacs
Dear Justin, I am sorry for the late reply. I still can't figure it out. Could you please send me the mdp file which was used for your single point calculations. I want to do some comparison and then solve the problem. Thanks very much! All the best, Qinghua -- View this message in context: http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012295.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] Re: Gromacs-4.6 on two Titans GPUs
I've gone to conclusion that simulation with 1 or 2 GPU simultaneously gave me the same performance mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test, mdrun -ntmpi 2 -ntomp 6 -gpu_id 0 -v -deffnm md_CaM_test, Doest it be due to the small CPU cores or addition RAM ( this system has 32 gb) is needed ? OR may be some extra options are needed in the config? James 2013/11/6 Richard Broadbent richard.broadben...@imperial.ac.uk Hi Dwey, On 05/11/13 22:00, Dwey Kauffman wrote: Hi Szilard, Thanks for your suggestions. I am indeed aware of this page. In a 8-core AMD with 1GPU, I am very happy about its performance. See below. My intention is to obtain a even better one because we have multiple nodes. ### 8 core AMD with 1 GPU, Force evaluation time GPU/CPU: 4.006 ms/2.578 ms = 1.554 For optimal performance this ratio should be close to 1! NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. Core t (s) Wall t (s)(%) Time: 216205.51027036.812 799.7 7h30:36 (ns/day)(hour/ns) Performance: 31.9560.751 ### 8 core AMD with 2 GPUs Core t (s) Wall t (s)(%) Time: 178961.45022398.880 799.0 6h13:18 (ns/day)(hour/ns) Performance: 38.5730.622 Finished mdrun on node 0 Sat Jul 13 09:24:39 2013 I'm almost certain that Szilard meant the lines above this that give the breakdown of where the time is spent in the simulation. Richard However, in your case I suspect that the bottleneck is multi-threaded scaling on the AMD CPUs and you should probably decrease the number of threads per MPI rank and share GPUs between 2-4 ranks. OK but can you give a example of mdrun command ? given a 8 core AMD with 2 GPUs. I will try to run it again. Regarding scaling across nodes, you can't expect much from gigabit ethernet - especially not from the cheaper cards/switches, in my experience even reaction field runs don't scale across nodes with 10G ethernet if you have more than 4-6 ranks per node trying to communicate (let alone with PME). However, on infiniband clusters we have seen scaling to 100 atoms/core (at peak). From your comments, it sounds like a cluster of AMD cpus is difficult to scale across nodes in our current setup. Let's assume we install Infiniband (20 or 40GB/s) in the same system of 16 nodes of 8 core AMD with 1 GPU only. Considering the same AMD system, what is a good way to obtain better performance when we run a task across nodes ? in other words, what dose mudrun_mpi look like ? Thanks, Dwey -- View this message in context: http://gromacs.5086.x6.nabble. com/Gromacs-4-6-on-two-Titans-GPUs-tp5012186p5012279.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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] nose-hoover vs v-rescale in implicit solvent
Does it make more sense to use nose-hoover or v-rescale when running in implicit solvent GBSA? I understand that this might be a matter of opinion. Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- 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
