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. Kind regards, Ehsan -- 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? Read http://www.gromacs.org/Support/Mailing_Lists
