[gmx-users] stopped simulation

Justin Lemkul jalemkul at vt.edu
Wed Nov 6 19:54:42 CET 2013



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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