[gmx-users] dt in mdp

[Alex]

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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