[gmx-users] stopped simulation
Mark Abraham
mark.j.abraham at gmail.com
Wed Nov 6 22:52:45 CET 2013
On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul <jalemkul at 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" <jalemkul at vt.edu> To:
>> "Discussion list for GROMACS users" <gmx-users at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
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