[gmx-users] dt in mdp

[Alex]

Dear Justin,
Any comment please?

Regards,
Alex

On Tue, Apr 7, 2020 at 5:38 PM Alex <alexanderwien2k at gmail.com> wrote:

> Thanks Justin for the response.
> Please find below the mdp file.
> The system is a thin film made out of a epoxy molecule, picture in be
> below link, with water on top and bottom of the film. I even sometimes have
> the same issue when I simulate the bulk of this system, I mean a cubic box
> filled by this molecule and no water.
> I got the force fields from the latest version of ATB repository by which
> I have previously done some other simulation for the same molecule.
>
> https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb
>
> %--------mdp-------
> title                    = Thin-Film
> integrator               = md
> dt                       = 0.002     ; 2 fs      ;0.001 1 fs
> nsteps                   = 25000000   ; 50 ns      ;50000000   ; 50 ns
> xtc-precision            = 500       ; 1000
> ;nstlist                  = 40
> %-----------------
> ;;in .trr file
> nstxout                  = 3000      ; 6000
> nstvout                  = 0
> nstfout                  = 0
> ;;in energy file.log
> nstlog                   = 2000       ; 4000
> nstcalcenergy            = 2000       ;4000
> nstenergy                = 2000         ;4000
> ;;in xtc file
> nstxout-compressed       = 0
> ;compressed-x-grps        = non-Water
> %-----------------
> continuation             = yes
> gen-vel                  = no
> constraint-algorithm     = lincs
> constraints              = h-bonds
> cutoff-scheme            = Verlet
> coulombtype              = PME
> rcoulomb                 = 1.4
>
> vdwtype                  = Cut-off
> rvdw                     = 1.4
> DispCorr                 = EnerPres
>
> tcoupl                    = v-rescale
> tc-grps                   = system
> tau-t                     = 1.5
> nhchainlength             = 10
> ref-t                     = 298.15
> pbc                       = xyz
>
> pcoupl                   = Parrinello-Rahman
> Pcoupltype               = isotropic
> tau_p                    = 2.5
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> refcoord-scaling         = com
> energygrps               = thin_film SOL
> comm-mode                = Linear
> nstcomm                  = 100
> comm-grps                = Thin_fiml SOL
> %-------------------------
>
> Thank you
> Alex
>
> On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/7/20 5:00 PM, Alex wrote:
>> > Dear all,
>> > After minimization and equalizations using nvt (v-rescale) and npt (both
>> > berendsen and ;Parrinello-Rahman), a simulation of mine could run well
>> for
>> > 200 ns using dt =0.001 while it would crash after 3 ns If I used dt =
>> 0.002
>> > with the particles communication fatal error.
>> >
>> > Fatal error:
>> > 2 particles communicated to PME rank 12 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.
>> >
>> > So, if the system would not be well equlibrated, then I would expect
>> that
>> > with dt = 0.001 the simulation wouldn't run well for 200 ns. But I
>> expect
>> > that it also crashes for example around 6 ns as the with the dt = 0.002
>> the
>> > simulation last only 3 ns.
>> >
>> > Any comment that helps to understand the problem would be highly
>> > appreciated.
>>
>> Please provide a description of what your system is and a full .mdp
>> file. While most of the time these crashes come from poor equilibration,
>> an inadequately parametrized topology or bad combination/misuse of
>> algorithms can also cause crashes.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>