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.
Re: [gmx-users] error in the middle of running mdrun_mpi
On 10/28/14 7:16 AM, Nizar Masbukhin wrote: 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. You can't do NPT with pbc = no, as your earlier .mdp files showed, so nothing can be scaled. -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.
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
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.
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
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 = 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 =
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] error in the middle of running mdrun_mpi
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 = 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
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
Re: [gmx-users] error in the middle of running mdrun_mpi
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 = 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
[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()
Re: [gmx-users] error in the middle of running mdrun_mpi
Hi, The warning message told you not to increase the table distance unless you were sure the table distance was the problem. Why were you sure the table distance was the problem, rather than some form of general instability of your system? In addition to all the usual reasons for http://www.gromacs.org/Documentation/Terminology/Blowing_Up, the GB kernels are completely untested, so you might try running with 4.5.7 (last version known to be probably-good for GB) to see whether the problem is in the code or your setup. Mark On Thu, Oct 23, 2014 at 10:38 PM, Nizar Masbukhin nizar.fku...@gmail.com wrote: 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]
