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 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. > -- 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.