[gmx-users] dt in mdp

[Alex]

On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/10/20 9:16 AM, Alex wrote:
> > 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.
>

By constraining all the bonds  "constraints = all-bonds", the simulation
crashes in the first step immediately irrespective to the starting point of
simulation, even if I continue the old working simulation.

Regards,
Alex

> >
> >
> >> 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
>
> I saw the conversation with David about this. I have nothing to add that
> he hasn't already said.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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