Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right?
Cheers, Ehsan ----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: > Hi gmx users, > > I have simulated ionomer in water solution using gromos force field. But in > middle of simulation(after 2 ns) the simulation stopped and I received these > messages: > > > WARNING: Listed nonbonded interaction between particles 174 and 188 > at distance 3f which is larger than the table limit 3f nm. > > This is likely either a 1,4 interaction, or a listed interaction inside > a smaller molecule you are decoupling during a free energy calculation. > Since interactions at distances beyond the table cannot be computed, > they are skipped until they are inside the table limit again. You will > only see this message once, even if it occurs for several interactions. > > IMPORTANT: This should not happen in a stable simulation, so there is > probably something wrong with your system. Only change the table-extension > distance in the mdp file if you are really sure that is the reason. > > Fatal error: > 1 particles communicated to PME node 5 are more than 2/3 times the cut-off > out of the domain decomposition cell of their charge group in dimension y. > This usually means that your system is not well equilibrated. > > > ---- > I used simulated annealing for equilibrating the system in NVT and NPT > condition. The mdp files are: > > ---- NVT ------ > > define = -DPOSRES > integrator = md > dt = 0.002 ; time step (in ps) > nsteps = 25000 ; Maximum number of steps to perform > > ; OUTPUT CONTROL OPTIONS > nstxout = 500 > nstvout = 500 > nstenergy = 500 > nstlog = 500 > energygrps = Non-Water Water > > ; NEIGHBORSEARCHING PARAMETERS > > nstlist = 1 > ns_type = grid > rlist = 1.5 > pbc = xyz > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > coulombtype= PME > pme_order = 4 > fourierspacing= 0.16 > rcoulomb = 1.5 > vdw-type = Cut-off > rvdw = 1.5 > > ; Temperature coupling > > tcoupl = v-rescale > tc-grps = Non-Water Water > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Dispersion correction > DispCorr = EnerPres > ; Pressure coupling is off > pcoupl = no > > ; Annealing > > annealing = single single > annealing-npoints = 5 5 > annealing-time = 0 10 20 30 40 0 10 20 30 40 > annealing-temp = 300 320 340 360 380 300 320 340 360 380 > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = yes > gen_temp = 300 > gen_seed = -1 > > ; OPTIONS FOR BONDS > constraints = ; all-bonds > continuation= no > constraint_algorithm = lincs > lincs_iter = 1 > lincs_order= 4 > > --------- NPT ------------ > > define = -DPOSRES > integrator = md > dt = 0.002 > nsteps = 25000 > > ; OUTPUT CONTROL OPTIONS > nstxout = 500 > nstvout = 500 > nstfout = 500 > nstenergy = 500 > nstlog = 500 > energygrps = Non-Water Water > > ; NEIGHBORSEARCHING PARAMETERS > > nstlist = 5 > ns_type = grid > rlist = 1.5 > pbc = xyz > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > coulombtype= PME > pme_order = 4 > fourierspacing= 0.16 > rcoulomb = 1.5 > vdw-type = Cut-off > rvdw = 1.5 > > ; Temperature coupling > > tcoupl = v-rescale > tc-grps = Non-Water Water > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Dispersion correction > DispCorr = EnerPres > > pcoupl = Parrinello-Rahman > Pcoupltype = Isotropic > tau_p = 2.0 > compressibility = 4.5e-5 > ref_p = 1.0 > refcoord_scaling = com > > ; Annealing > > annealing = single single > annealing-npoints = 5 5 > annealing-time = 0 10 20 30 40 0 10 20 30 40 > annealing-temp = 380 360 340 320 300 380 360 340 320 300 > > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = no > > ; OPTIONS FOR BONDS > constraints = ; all-bonds > continuation= yes ;continuation from NVT > constraint_algorithm = lincs > lincs_iter = 1 > lincs_order= 4 > -------------------------- > > Is the equilibration time is long enough? I appreciate any help/suggestion > regarding my case. > The cutoffs values (1.5) are wrong for using any of the Gromos parameter sets. Likely the dynamics have become unstable due to violation of the physical model. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? 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