[gmx-users] dt in mdp
Alex
alexanderwien2k at gmail.com
Fri Apr 10 15:17:16 CEST 2020
Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/10/20 8:13 AM, Alex wrote:
> > Dear Justin,
> > Any comment please?
>
> Sorry, haven't had power/network for a while due to some bad storms here.
>
> GROMOS force fields are parametrized assuming all bonds are fixed, so
> your constraints should be "all-bonds" not "h-bonds."
>
Interesting, hopefully that is the problem.
>
> I would also suggest you thoroughly validate the quality of the epoxy
> molecule topology against QM data and bulk-phase properties, if possible.
>
As the ATB folks claim, the parameterization has been performed against a
very high level DFT calculation, especially for the molecules with less
than 50 atoms.
I already have tested the density and it is in agreement with the
experimental value.
Regarding the "comm-grps = " , would you also please kindly let me know
which one you would recommend for this system + plus a small single
molecule called MOL_A which defuses from water inside the epoxy, specially
for the PMF calculation of the Mol_A?
comm-grps = Other SOL ;; (Other = thin_film and Mol_A)
or
comm-grps = system
Thank you
Alex
>
> -Justin
>
> > 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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> --
> ==================================================
>
> 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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