On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: > >> 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? >> >> > No. The cutoff value is not a function of box size; it is a fixed > property of the force field. No wonder the simulation is crashing. If > your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting > interactions across PBC! > Triple counting is not possible, per minimum-image convention. I think Ehsan's report of a "0.5nm" box size is probably wrong, e.g. per its documentation, editconf -d 0.5 does not produce a 0.5nm box. Mark Refer to the primary literature for the Gromos parameter set you are using > for proper settings. You haven't said which one you're using, and there > may be slight differences between them. If the value you're using isn't > taken directly from a paper, it's not credible. > > -Justin > > > 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. 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