[gmx-users] can't generate pdb file in g_cluster
hi gromacs users, while i was trying to cluster structure using: g_cluster_mpi -f traj -s chainB.pdb -method gromos -cl out.pdb -n index_20-29_ca.ndx error message appeared [nizars-mbp:01757] *** Process received signal *** [nizars-mbp:01757] Signal: Segmentation fault: 11 (11) [nizars-mbp:01757] Signal code: Address not mapped (1) [nizars-mbp:01757] Failing at address: 0x0 [nizars-mbp:01757] [ 0] 0 libsystem_platform.dylib 0x7fff924485aa _sigtramp + 26 [nizars-mbp:01757] [ 1] 0 ??? 0x2060 0x0 + 35596688949248 [nizars-mbp:01757] *** End of error message *** this wasn't happening if i am not using -cl flag. what is libsystem_platform.dylib ? do i miss some library? -- Thanks My Best Regards, Nizar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error while executing do_dssp program
hi gromacs user, when i try to compute secondary structure using do_dssp program, the error message appear: Program do_dssp_mpi, VERSION 5.0.2 Source code file: /home/user/gromacs-5.0.2/src/gromacs/fileio/futil.cpp, line: 863 Fatal error: Permission denied for opening ddhCTh1r For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; i have installed dssp program, and i have set the environment DSSP to the path where i install DSSP. could anyone please explain to me whats wrong? -- Thanks My Best Regards, Nizar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error while executing do_dssp program
the directory where i execute the command is in desktop. i think that folder doesnt need write/read permission. i even have used sudo -s mode, still the problem exist. On Dec 31, 2014 11:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/31/14 10:53 AM, Nizar Masbukhin wrote: hi gromacs user, when i try to compute secondary structure using do_dssp program, the error message appear: Program do_dssp_mpi, VERSION 5.0.2 Source code file: /home/user/gromacs-5.0.2/src/gromacs/fileio/futil.cpp, line: 863 Fatal error: Permission denied for opening ddhCTh1r For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; i have installed dssp program, and i have set the environment DSSP to the path where i install DSSP. could anyone please explain to me whats wrong? You don't have write permission in the directory where you are executing your command. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Continuing inturepted REMD simulation
So, in REMD case, we can not continue simulation if it interrupted? and, How do I check wether exchange occurred or not? On Tue, Dec 2, 2014 at 7:31 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You'll certainly lose the per-run statistics, because nobody's cared enough to write the code to accumulate it over interrupted runs. Showing no exchanges at all is another problem, but *you should look at the actual exchange reports to see whether the problem is that no exchanges* occurred, or that the books weren't being kept properly. Mark On Tue, Dec 2, 2014 at 6:59 AM, Nizar Masbukhin nizar.fku...@gmail.com wrote: Dear gromacs users, I have finished an REMD simulation, tough it had interupted (by electrical instabilty that lead computer shutdown) several times. I continue the interupted simulation using this command: mpirun -np 8 mdrun_mpi -v -multidir md[01234567] -replex 2000 -cpt 3 -cpi state.cpt however, the remd statistics show unexpected exchange probability. Replica exchange statistics Repl 3365 attempts, 1683 odd, 1682 even Repl average probabilities: Repl 01234567 Repl Repl number of exchanges: Repl 01234567 Repl0000000 Repl average number of exchanges: Repl 01234567 Repl .00 .00 .00 .00 .00 .00 .00 ReplEmpirical Transition Matrix Repl 1 2 3 4 5 6 7 8 Repl 1. 0. 0. 0. 0. 0. 0. 0. 0 Repl 0. 1. 0. 0. 0. 0. 0. 0. 1 Repl 0. 0. 1. 0. 0. 0. 0. 0. 2 Repl 0. 0. 0. 1. 0. 0. 0. 0. 3 Repl 0. 0. 0. 0. 1. 0. 0. 0. 4 Repl 0. 0. 0. 0. 0. 1. 0. 0. 5 Repl 0. 0. 0. 0. 0. 0. 1. 0. 6 Repl 0. 0. 0. 0. 0. 0. 0. 1. 7 That statistics was very different when i try remd simulation with short timesteps, and uninterupted one. the exchange probabilty was 0.3 as i expected. Could anyone tell me whats wrong? -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Continuing inturepted REMD simulation
Dear gromacs users, I have finished an REMD simulation, tough it had interupted (by electrical instabilty that lead computer shutdown) several times. I continue the interupted simulation using this command: mpirun -np 8 mdrun_mpi -v -multidir md[01234567] -replex 2000 -cpt 3 -cpi state.cpt however, the remd statistics show unexpected exchange probability. Replica exchange statistics Repl 3365 attempts, 1683 odd, 1682 even Repl average probabilities: Repl 01234567 Repl Repl number of exchanges: Repl 01234567 Repl0000000 Repl average number of exchanges: Repl 01234567 Repl .00 .00 .00 .00 .00 .00 .00 ReplEmpirical Transition Matrix Repl 1 2 3 4 5 6 7 8 Repl 1. 0. 0. 0. 0. 0. 0. 0. 0 Repl 0. 1. 0. 0. 0. 0. 0. 0. 1 Repl 0. 0. 1. 0. 0. 0. 0. 0. 2 Repl 0. 0. 0. 1. 0. 0. 0. 0. 3 Repl 0. 0. 0. 0. 1. 0. 0. 0. 4 Repl 0. 0. 0. 0. 0. 1. 0. 0. 5 Repl 0. 0. 0. 0. 0. 0. 1. 0. 6 Repl 0. 0. 0. 0. 0. 0. 0. 1. 7 That statistics was very different when i try remd simulation with short timesteps, and uninterupted one. the exchange probabilty was 0.3 as i expected. Could anyone tell me whats wrong? -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding simulated tempering
Dear gromacs users, Simulated tempering, one of multi canonical MC method, can be performed in GROMACS. As I know, adaptive tempering is also multi canonical ensemble method. Can adaptive tempering be performed in GROMACS? Or both of them are the same? -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University, Malang, Indonesia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] md.log interpretation
I have tried running simulation with zero cutoff and zero nstlist and simple ns. That was very very slow, however. anyway thanks for the reply. On Nov 5, 2014 9:38 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I am not familiar with the implementation details, but I would assume there is a dependency on rcoulomb of the cost of the Born force chain rule. You can check this by trying different values. It might be faster to use infinite cutoffs (see manual) so that the algorithm does not need to search. Mark On Tue, Nov 4, 2014 at 1:34 AM, Nizar Masbukhin nizar.fku...@gmail.com wrote: Dear gromacs users, I've just finished my NVT equilibration in implicit solvent. From md.log, i see that most of time were used to calculate Forces (of Born force chain rule). Could someone explain to me why calculating it takes so long? mdp setting: integrator=md dt=0.004 nstep=250 bd-frict=50 rlist=5 rvdw=5 rcoulomb=5 nstlist=40 implicit-solvent=GBSA gb-alogarithm=still nstgbradii=40 gbradii=5 gb-epsilon-solvent=80 gb-salt-conc=0.2 sa-algorithm=ace-approximation sa-surface-tension=2.05 constraints=all-bonds constraints-algorithm=LINCS lincs-order=12 md.log M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - NB VdW [VF] 32677.013279 32677.013 0.0 NB VdW [F] 1740991.575264 1740991.575 0.3 NB VdW Elec. [VF] 1192677.312698 1192677.313 0.2 NB VdW Elec. [F] 106409048.599622 106409048.600 17.9 1,4 nonbonded interactions 20035.628466 1803206.562 0.3 Born radii (Still) 1999216.23274293963162.939 15.8 Born force chain rule 25548182.811729 *383222742.176* 64.4 NS-Pairs 64906.572700 1363038.027 0.2 CG-CoM 205.506576 616.520 0.0 Propers 15168.313980 3473543.901 0.6 Impropers 637.980588 132699.962 0.0 Pos. Restr. 3830.053530 191502.676 0.0 Virial 82.6954711488.518 0.0 Stop-CM 82.214752 822.148 0.0 Calc-Ekin 822.011152 22194.301 0.0 Lincs 4696.969329 281818.160 0.0 Lincs-Mat 229529.791548 918119.166 0.2 Constraint-V 9393.938658 75151.509 0.0 Constraint-Vir 46.9739791127.375 0.0 Virtual Site 3 615.868824 22787.146 0.0 Virtual Site 3fd 791.205144 75164.489 0.0 Virtual Site 3fad 168.761208 29701.973 0.0 Virtual Site 3out 1893.632256 164746.006 0.0 Virtual Site 4fdn 576.418152 146410.211 0.0 (null) 476.315439 0.000 0.0 - Total 595265438.267 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G On 1 MPI rank Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Vsite constr. 111085001 96.421385.432 0.2 Neighbor search11 27126 915.964 3661.462 2.1 Force 111085001 *39317.742* 157168.118 91.3 Vsite spread 111095852 142.563569.880 0.3 Write traj.11 11030 425.764 1701.942 1.0 Update 111085001 96.742386.714 0.2 Constraints1110850011311.720 5243.449 3.0 Rest 766.404 3063.612 1.8 - Total 43073.320 172180.608 100.0
[gmx-users] md.log interpretation
Dear gromacs users, I've just finished my NVT equilibration in implicit solvent. From md.log, i see that most of time were used to calculate Forces (of Born force chain rule). Could someone explain to me why calculating it takes so long? mdp setting: integrator=md dt=0.004 nstep=250 bd-frict=50 rlist=5 rvdw=5 rcoulomb=5 nstlist=40 implicit-solvent=GBSA gb-alogarithm=still nstgbradii=40 gbradii=5 gb-epsilon-solvent=80 gb-salt-conc=0.2 sa-algorithm=ace-approximation sa-surface-tension=2.05 constraints=all-bonds constraints-algorithm=LINCS lincs-order=12 md.log M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) VF=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - NB VdW [VF] 32677.013279 32677.013 0.0 NB VdW [F] 1740991.575264 1740991.575 0.3 NB VdW Elec. [VF] 1192677.312698 1192677.313 0.2 NB VdW Elec. [F] 106409048.599622 106409048.60017.9 1,4 nonbonded interactions 20035.628466 1803206.562 0.3 Born radii (Still) 1999216.23274293963162.93915.8 Born force chain rule 25548182.811729 *383222742.176*64.4 NS-Pairs 64906.572700 1363038.027 0.2 CG-CoM 205.506576 616.520 0.0 Propers 15168.313980 3473543.901 0.6 Impropers 637.980588 132699.962 0.0 Pos. Restr. 3830.053530 191502.676 0.0 Virial 82.6954711488.518 0.0 Stop-CM 82.214752 822.148 0.0 Calc-Ekin 822.011152 22194.301 0.0 Lincs 4696.969329 281818.160 0.0 Lincs-Mat 229529.791548 918119.166 0.2 Constraint-V 9393.938658 75151.509 0.0 Constraint-Vir 46.9739791127.375 0.0 Virtual Site 3 615.868824 22787.146 0.0 Virtual Site 3fd 791.205144 75164.489 0.0 Virtual Site 3fad 168.761208 29701.973 0.0 Virtual Site 3out 1893.632256 164746.006 0.0 Virtual Site 4fdn 576.418152 146410.211 0.0 (null) 476.315439 0.000 0.0 - Total 595265438.267 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G On 1 MPI rank Computing: Num Num CallWall time Giga-Cycles Ranks Threads Count (s) total sum% - Vsite constr. 111085001 96.421385.432 0.2 Neighbor search11 27126 915.964 3661.462 2.1 Force 111085001 *39317.742* 157168.118 91.3 Vsite spread 111095852 142.563569.880 0.3 Write traj.11 11030 425.764 1701.942 1.0 Update 111085001 96.742386.714 0.2 Constraints1110850011311.720 5243.449 3.0 Rest 766.404 3063.612 1.8 - Total 43073.320 172180.608 100.0 - Core t (s) Wall t (s)(%) Time:41985.82843073.320 97.5 11h57:53 (ns/day)(hour/ns) Performance:8.7062.757 Finished mdrun on rank 0 Tue Nov 4 03:27:26 2014 I know, for someone this question is less important, but for me performance is important. -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
Re: [gmx-users] Free energy in implicit solvent
even using PLUMED plugin? On Wed, Oct 29, 2014 at 1:59 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2014-10-29 01:05, Nizar Masbukhin wrote: Dear gromacs users, Is it possible to calculate free energy in implicit solvent in gromacs? It is not possible at all. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in the middle of running mdrun_mpi
Thank you very much Justin and Mark. On Tue, Oct 28, 2014 at 2:31 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Oct 27, 2014 at 6:05 PM, Nizar Masbukhin nizar.fku...@gmail.com wrote: i dont really understand the point. could you please what do you mean in the last reply? what command should i use? if, say i have 72 cores in 9 nodes, and 16 replicas to simulate in implicit solvent. Hi, You can only use two MPI ranks per replica if there's a limit of two ranks per simulation. So that's 32 ranks total. So something like mpirun -np 32 mdrun_mpi -multidir your-16-directories -repl_ex whatever after setting up the MPI environment to fill four nodes. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in the middle of running mdrun_mpi
Now, the only thing worrying me is a warning Turning off pressure coupling for vacuum system on NPT equilibration. Can I just ignore this warning or should i do something? as i didn't mean my system in vacuum. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Free energy in implicit solvent
Dear gromacs users, Is it possible to calculate free energy in implicit solvent in gromacs? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in the middle of running mdrun_mpi
and how to use that 2 cores? i think that would increase performace twice as now i am running 1 core per replica. On Mon, Oct 27, 2014 at 7:15 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/26/14 9:55 AM, Nizar Masbukhin wrote: regarding gaining speed in implicit solvent simulation, i have tried to parallelize using -ntmpi flag. However gromacs doesn't allow as i use group cutoff-scheme. Any recommendation how to parallelise implicit solvent simulation? I do need parallelise my simulation. I have found the same question in this mail list, one suggest use all-vs-all kernel which uses zero cut-off. This is my test run actually. I intend to run my simulation in cluster computer. Unless the restriction was lifted at some point, implicit simulations won't run on more than 2 cores. There were issues with constraints that led to the limitation. -Justin On Sun, Oct 26, 2014 at 8:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/26/14 9:17 AM, Nizar Masbukhin wrote: Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. Longer cutoffs mean there are more interactions to calculate, but the cutoffs aren't to be toyed with arbitrarily to gain speed. They are a critical element of the force field itself, though in implicit solvent, it is common to increase (and never decrease) the cutoff values used in explicit solvent. Physical validity should trump speed any day. -Justin On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog
Re: [gmx-users] error in the middle of running mdrun_mpi
i dont really understand the point. could you please what do you mean in the last reply? what command should i use? if, say i have 72 cores in 9 nodes, and 16 replicas to simulate in implicit solvent. On 10/27/14 5:59 AM, Nizar Masbukhin wrote: and how to use that 2 cores? i think that would increase performace twice as now i am running 1 core per replica. In the context of REMD, mdrun should figure this out if you issue the command over 2N processors, where N is the number of replicas. -Justin On Mon, Oct 27, 2014 at 7:15 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/26/14 9:55 AM, Nizar Masbukhin wrote: regarding gaining speed in implicit solvent simulation, i have tried to parallelize using -ntmpi flag. However gromacs doesn't allow as i use group cutoff-scheme. Any recommendation how to parallelise implicit solvent simulation? I do need parallelise my simulation. I have found the same question in this mail list, one suggest use all-vs-all kernel which uses zero cut-off. This is my test run actually. I intend to run my simulation in cluster computer. Unless the restriction was lifted at some point, implicit simulations won't run on more than 2 cores. There were issues with constraints that led to the limitation. -Justin On Sun, Oct 26, 2014 at 8:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/26/14 9:17 AM, Nizar Masbukhin wrote: Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. Longer cutoffs mean there are more interactions to calculate, but the cutoffs aren't to be toyed with arbitrarily to gain speed. They are a critical element of the force field itself, though in implicit solvent, it is common to increase (and never decrease) the cutoff values used in explicit solvent. Physical validity should trump speed any day. -Justin On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm
Re: [gmx-users] error in the middle of running mdrun_mpi
Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 1 ns-type = simple pbc = no rlist = 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw= 0.5 table-extension = 1 fourierspacing = 0.12 fourier-nx= 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = Nose-Hoover tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = parrinello-rahman pcoupltype = Isotropic tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 refcoord-scaling = No gen-vel = no gen-temp = 298.00 gen-seed = -1 constraints = all-bonds constraint-algorithm = Lincs continuation = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for MD* integrator = md tinit = 0 dt = 0.001 nsteps = 5 ; 1 us init-step = 0 simulation-part= 1 comm-mode = Angular nstcomm = 100 comm-grps = system bd-fric = 0 ld-seed = -1 nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstcalcenergy = 1 nstenergy
Re: [gmx-users] error in the middle of running mdrun_mpi
regarding gaining speed in implicit solvent simulation, i have tried to parallelize using -ntmpi flag. However gromacs doesn't allow as i use group cutoff-scheme. Any recommendation how to parallelise implicit solvent simulation? I do need parallelise my simulation. I have found the same question in this mail list, one suggest use all-vs-all kernel which uses zero cut-off. This is my test run actually. I intend to run my simulation in cluster computer. On Sun, Oct 26, 2014 at 8:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/26/14 9:17 AM, Nizar Masbukhin wrote: Thanks Justin. I have increased the cutoff, and yeah thats work. There were no error message anymore. The first 6 nanoseconds, i felt the simulation run slower. Felt so curious that simulation run very fast the rest of time. Longer cutoffs mean there are more interactions to calculate, but the cutoffs aren't to be toyed with arbitrarily to gain speed. They are a critical element of the force field itself, though in implicit solvent, it is common to increase (and never decrease) the cutoff values used in explicit solvent. Physical validity should trump speed any day. -Justin On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 8:31 AM, Nizar Masbukhin wrote: Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 1 ns-type = simple pbc = no rlist = 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw= 0.5 table-extension = 1 fourierspacing = 0.12 fourier-nx= 0 fourier-ny = 0 fourier-nz
Re: [gmx-users] installing on macbook
Hi Suraya. I have succesfully installed Gromacs 4.5, 4.6, and 5.0 on my macbook pro running OS X Mavericks, even with CUDA support. I am not using apple compiler because apple compiler in Mavericks (clang 3.4) doesn't support OpenMP, that will cause many errors when compiling gromacs (my experience) so that i use gcc 4.7 compiler instead. Here my step to install Gromacs on My MacbookPro mid 2009. FIRST: -Install GCC/G++ 4.7. Its very easy to install gcc/g++ 4.7 via MacPorts ( www.macports.org) because it is almost automatic as all dependencies will be installed. SECOND: -Download Gromacs 5.0/5.0.01/5.0.2 -Extract the downloaded file -open the downloaded folder in terminal. If you don't familiar how to open folder in terminal, then just right click - service -- new terminal at folder (if this options doesn't exists, do the following steps : system preferences -- keyboard -- shortcut -- service -- new folder at terminal) - just type: *cmake .. -DCMAKE_C_COMPILER=/opt/local/bin/gcc -DCMAKE_CXX_COMPILER=/opt/local/bin/g++ -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_BUILD_OWN_FFTW=ON *then press return/enter. - everything should be set up, and the fftw is also automatically downloaded and compiled. - then type *make -j 2 *(if your macbook has 2 cores) - then * make install* - run *make check *if you compile 5.0.2 - then type *export PATH=$PATH:/usr/local/gromacs/bin/* every time you want to start gromacs that's it. good luck On Fri, Oct 24, 2014 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/14 6:32 AM, Suraya Abdul Sani wrote: hi.. i have problem in installing gromacs in my macbook pro ( personal pc) .. can anyone help me with this?? Not unless you tell us exactly what you're doing - exact cmake command, exact error messages, etc. In general, follow http://www.gromacs.org/Documentation/Installation_ Instructions -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in the middle of running mdrun_mpi
Thanks for yor reply, Mark. At first i was sure that the problem was table-exension because when I enlarge table-extension value, warning message didn't appear anymore. Besides, i have successfully minimized and equilibrated the system (indicated by Fmax emtol reached; and no error messages during NVTNPT equilibration, except a warning that the Pcouple is turned off in vacuum system). However, the error message appeared without table-extension warning makes me doubt also about my system stability. Here is my mdp setting. Please tell me if there are any 'weird' setting, and also kindly suggest/recommend a better setting. *mdp file for Minimisation* integrator = steep nsteps = 5000 emtol = 200 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 cutoff-scheme = group nstlist = 1 ns_type = simple pbc = no rlist = 0.5 coulombtype = cut-off rcoulomb = 0.5 vdw-type = cut-off rvdw-switch = 0.8 rvdw = 0.5 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no tcoupl = no pcoupl = no free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = none constraint-algorithm = lincs continuation = no lincs-order = 12 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 *mdp file for NVT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 25 init-step = 0 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 5 nstfout = 5 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme= group nstlist = 1 ns-type = simple pbc= no rlist= 0.5 coulombtype = cut-off rcoulomb= 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch= 0.8 rvdw = 0.5 table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 refcoord-scaling = No gen-vel = yes gen-temp = 298.00 gen-seed = -1 constraints= all-bonds constraint-algorithm = Lincs continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for NPT equilibration* define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 50 init-step = 0 simulation-part = 1 comm-mode = angular nstcomm = 100 bd-fric = 0 ld-seed = -1 nstxout = 1000 nstvout = 50 nstfout = 50 nstlog = 100 nstcalcenergy = 100 nstenergy = 1000 nstxtcout = 100 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 1 ns-type = simple pbc = no rlist = 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw= 0.5 table-extension = 1 fourierspacing = 0.12 fourier-nx= 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80 sa-algorithm = Ace-approximation sa-surface-tension = 2.05 tcoupl = Nose-Hoover tc-grps = system tau-t = 0.1 ref-t = 298.00 pcoupl = parrinello-rahman pcoupltype = Isotropic tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 refcoord-scaling = No gen-vel = no gen-temp = 298.00 gen-seed = -1 constraints = all-bonds constraint-algorithm = Lincs continuation = yes Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 *mdp file for MD* integrator = md tinit = 0 dt = 0.001 nsteps = 5 ; 1 us init-step = 0 simulation-part= 1 comm-mode = Angular nstcomm = 100 comm-grps = system bd-fric = 0 ld-seed = -1 nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1 nstcalcenergy = 1 nstenergy = 1 nstxtcout = 0 xtc-precision = 1000 xtc-grps = system energygrps = system cutoff-scheme = group nstlist = 10 ns-type = simple pbc = no rlist= 0.5 coulombtype= cut-off rcoulomb = 0.5 vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet rvdw-switch = 0.8 rvdw = 0.5 DispCorr = No table-extension = 500 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 implicit-solvent = GBSA ;implicit-solvent = GBSA gb-algorithm = still nstgbradii = 1 rgbradii = 0.5 gb-epsilon-solvent = 80
[gmx-users] error in the middle of running mdrun_mpi
Dear gromacs users, I try simulate protein folding using REMD sampling method in implicit solvent. I run my simulation on MPI-compiled gromacs 5.0.2 on single node. I have succesfully minimized equilibrated (NVT-constrained, and NPT constrained) my system. However, In the middle of mdrun_mpi process, the warning messages appear. *starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.5 steps, 50.0 ps.step 2873100, will finish Sat Nov 1 10:03:07 2014WARNING: Listed nonbonded interaction between particles 192 and 197at distance 16.773 which is larger than the table limit 10.500 nm.This is likely either a 1,4 interaction, or a listed interaction insidea 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 willonly see this message once, even if it occurs for several interactions.IMPORTANT: This should not happen in a stable simulation, so there isprobably something wrong with your system. Only change the table-extensiondistance in the mdp file if you are really sure that is the reason.* *[nizarPC:07548] *** Process received signal ***[nizarPC:07548] Signal: Segmentation fault (11)[nizarPC:07548] Signal code: Address not mapped (1)[nizarPC:07548] Failing at address: 0x1ef8d90[nizarPC:07548] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30) [0x7f610bc9fc30][nizarPC:07548] [ 1] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_single+0x836) [0x7f610d3a2466][nizarPC:07548] [ 2] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(do_nonbonded+0x240) [0x7f610d235a30][nizarPC:07548] [ 3] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(do_force_lowlevel+0x1d3e) [0x7f610d97bebe][nizarPC:07548] [ 4] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(do_force_cutsGROUP+0x1510) [0x7f610d91bbe0][nizarPC:07548] [ 5] mdrun_mpi(do_md+0x57c1) [0x42e5e1][nizarPC:07548] [ 6] mdrun_mpi(mdrunner+0x12a1) [0x413af1][nizarPC:07548] [ 7] mdrun_mpi(_Z9gmx_mdruniPPc+0x18e5) [0x4337b5][nizarPC:07548] [ 8] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x92) [0x7f610ce15a42][nizarPC:07548] [ 9] mdrun_mpi(main+0x7c) [0x40cb8c][nizarPC:07548] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f610bc8aec5][nizarPC:07548] [11] mdrun_mpi() [0x40ccce][nizarPC:07548] *** End of error message ***--mpirun noticed that process rank 5 with PID 7548 on node nizarPC exited on signal 11 (Segmentation fault).* I have increased the table-extension to 500.00 (how much this value should be?), and re-grompp and mdrun again. there were no warning message regarding table-extension anymore, However, this error messages showed: *starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.5 steps, 50.0 ps.step 4142800, will finish Sat Nov 1 10:35:55 2014[nizarPC:09984] *** Process received signal ***[nizarPC:09984] Signal: Segmentation fault (11)[nizarPC:09984] Signal code: Address not mapped (1)[nizarPC:09984] Failing at address: 0x1464040[nizarPC:09984] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30) [0x7fa764b65c30][nizarPC:09984] [ 1] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_single+0x85f) [0x7fa76626848f][nizarPC:09984] [ 2] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(do_nonbonded+0x240) [0x7fa7660fba30][nizarPC:09984] [ 3] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(do_force_lowlevel+0x1d3e) [0x7fa766841ebe][nizarPC:09984] [ 4] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(do_force_cutsGROUP+0x1510) [0x7fa7667e1be0][nizarPC:09984] [ 5] mdrun_mpi(do_md+0x57c1) [0x42e5e1][nizarPC:09984] [ 6] mdrun_mpi(mdrunner+0x12a1) [0x413af1][nizarPC:09984] [ 7] mdrun_mpi(_Z9gmx_mdruniPPc+0x18e5) [0x4337b5][nizarPC:09984] [ 8] /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x92) [0x7fa765cdba42][nizarPC:09984] [ 9] mdrun_mpi(main+0x7c) [0x40cb8c][nizarPC:09984] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fa764b50ec5][nizarPC:09984] [11] mdrun_mpi()
[gmx-users] Add missing residue
Dear users, I'm going to simulate a protein. On the pdb file contents, it's said that this protein has two chains, and missing residues and atoms. when I try to pdb2gmx, the error messages occured. It seemed due tue the missing residue so that i got the message error. My question is: How can I add missing resiudes and atoms to the pdb files so that i can use it? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Add missing residue
Thanks Mark, I will try swiss-Pdb viewer. On Sun, Sep 28, 2014 at 9:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, There are some suggestions at http://www.gromacs.org/Documentation/File_Formats/Coordinate_File Mark On Sun, Sep 28, 2014 at 4:35 PM, Nizar Masbukhin nizar.fku...@gmail.com wrote: Dear users, I'm going to simulate a protein. On the pdb file contents, it's said that this protein has two chains, and missing residues and atoms. when I try to pdb2gmx, the error messages occured. It seemed due tue the missing residue so that i got the message error. My question is: How can I add missing resiudes and atoms to the pdb files so that i can use it? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] overclocked cpu on gromacs
hello all, i am wondering that using overclocked cpu on gromas is safe, in terms of results reability. and is there any benefit from xeon processor compared to non xeon? and is there any benedit from ECC memory on gromacs? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error message in mdrun: Check for bad contacts and/or reduce the timestep if appropriate.
Hi friends, I am calculating free energy of a protein. I got this message when i run mdrun. My command was mdrun -deffnm npt -nt 1 Step 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.22, max 0.000500 (between atoms 2240 and 2243) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2844 2845 39.80.1105 0.1090 0.1090 step 2: Water molecule starting at atom 41058 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I have reduced nsteps from 5000 to 1, but the same error message appeared = My Best Regards, Nizar Medical Faculty of Brawijaya University, Malang, Indonesia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem with pdb2gmx
Hi, friends. I’m new to gromacs. I’m trying to learn it based on tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html. Whenever i input pdb2gmx line, i always get this message: Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading 1AKI.pdb... --- Program pdb2gmx, VERSION 4.5.5 Source code file: futil.c, line: 491 File input/output error: 1AKI.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- What is wrong? can anyone explain? Thank for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem with pdb2gmx
Hi, friends. I’m new to gromacs. I’m trying to learn it based on tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html. Whenever i input pdb2gmx line, i always get this message: Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading 1AKI.pdb... --- Program pdb2gmx, VERSION 4.5.5 Source code file: futil.c, line: 491 File input/output error: 1AKI.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- What is wrong? can anyone explain? and what is the solution? Thank for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem with pdb2gmx
i wrote this pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce On May 1, 2014, at 5:28 PM, Chandan Choudhury iitd...@gmail.com wrote: On Thu, May 1, 2014 at 3:32 PM, Nizar Masbukhin nizar.fku...@gmail.comwrote: Hi, friends. I’m new to gromacs. I’m trying to learn it based on tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html . Whenever i input pdb2gmx line, i always get this message: Using the Oplsaa force field in directory oplsaa.ff Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/ aminoacids.r2b Reading 1AKI.pdb... --- Program pdb2gmx, VERSION 4.5.5 Source code file: futil.c, line: 491 File input/output error: 1AKI.pdb For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- What is wrong? can anyone explain? and what is the solution? Please copy and paste your command. It seems that there is some problem in the pdb file (1AKI). You can check its contents. Chandan Thank for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
