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 NVT&NPT >>>> 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 = 250000 >>>> >>>> init-step = 0 >>>> >>>> comm-mode = angular >>>> >>>> nstcomm = 100 >>>> >>>> bd-fric = 0 >>>> >>>> ld-seed = -1 >>>> >>>> nstxout = 1000 >>>> >>>> nstvout = 50000 >>>> >>>> nstfout = 50000 >>>> >>>> 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 = 500000 >>>> >>>> init-step = 0 >>>> >>>> simulation-part = 1 >>>> >>>> comm-mode = angular >>>> >>>> nstcomm = 100 >>>> >>>> bd-fric = 0 >>>> >>>> ld-seed = -1 >>>> >>>> nstxout = 1000 >>>> >>>> nstvout = 500000 >>>> >>>> nstfout = 500000 >>>> >>>> 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 = 500000000 ; 1 us >>>> >>>> init-step = 0 >>>> >>>> simulation-part= 1 >>>> >>>> comm-mode = Angular >>>> >>>> nstcomm = 100 >>>> >>>> comm-grps = system >>>> >>>> bd-fric = 0 >>>> >>>> ld-seed = -1 >>>> >>>> nstxout = 10000 >>>> >>>> nstvout = 0 >>>> >>>> nstfout = 0 >>>> >>>> nstlog = 10000 >>>> >>>> nstcalcenergy = 10000 >>>> >>>> nstenergy = 10000 >>>> >>>> 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 >>>> >>>> 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 = no >>>> >>>> gen-temp = 298.00 >>>> >>>> gen-seed = -1 >>>> >>>> constraints = none >>>> >>>> constraint-algorithm = Lincs >>>> >>>> continuation = yes >>>> >>>> Shake-SOR = no >>>> >>>> shake-tol = 0.0001 >>>> >>>> lincs-order = 4 >>>> >>>> lincs-iter = 1 >>>> >>>> lincs-warnangle = 30 >>>> >>>> morse = no >>>> >>>> free-energy = yes >>>> >>>> couple-lambda0 = vdw-q >>>> >>>> couple-lambda1= vdw-q >>>> >>>> couple-intramol = no >>>> >>>> init-lambda = 0 >>>> >>>> delta-lambda = 0.1 >>>> >>>> nstdhdl = 50 >>>> >>>> calc-lambda-neighbors = 1 >>>> >>>> dhdl-print-energy = no >>>> >>>> sc-alpha = 0 >>>> >>>> sc-power= 1 >>>> >>>> sc-r-power = 6 >>>> >>>> sc-sigma= 0.3 >>>> >>>> sc-coul = no >>>> >>>> separate-dhdl-file = yes >>>> >>>> dhdl-derivatives = yes >>>> >>>> dh_hist_size = 0 >>>> >>>> dh_hist_spacing = 0.1 >>>> >>>> >>>> You need to simplify significantly to determine what the issue is. >>> You're >>> using (1) very short cutoffs, (2) free energy, and (3) implicit solvent. >>> Any combination of those might be causing the problem you're having. >>> Generally, extra long cutoffs are used in implicit environments. Try a >>> "normal" run without the free energy code going and see if that improves >>> the situation. >>> >>> -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. >>> >>> >> >> >> > -- > ================================================== > > 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.
