[gmx-users] stopped simulation

[Justin Lemkul]

On 11/6/13 2:27 PM, Ehsan Sadeghi wrote:
> What is this cut-off radius mentioned in the manual? The cut-off radius used
> to truncate non-bonded inter-actions may not exceed half the shortest box
> vector.
>

It refers to the longest cutoff used to evaluate nonbonded interactions, 
whatever that may be for your chosen force field.

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

-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 11:22:09 AM Subject: Re: [gmx-users] stopped simulation
>
>
>
> 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!
>
> 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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