[gmx-users] MD simullations with Morse potential

[Tsjerk Wassenaar]

Hi Qinghua,

I have run simulations with morse bonds a while back, in combination with
the Gromos 45a3 force field. I only had a few of those bonds, though.

Which Gromacs version are you using and which force field?

Cheers,

Tsjerk
On Apr 27, 2014 10:44 AM, "fantasticqhl" <fantasticqhl at gmail.com> wrote:

> Hi Justin,
>
> Thanks very much for your reply! Regarding to your two explanations, I
> guess it might be the first one.
> I have also tried to do a simulation of a three-residue (Gly-Ser-Asn)
> system with water, but it still did not work.
>
>
> Could you also give some test for this morse potential? Thanks very much!
>
>
> All the best,
> Qinghua
>
>
>
>
> On 04/26/2014 12:31 AM, Justin Lemkul [via GROMACS] wrote:
> >
> >
> > On 4/25/14, 5:37 PM, fantasticqhl wrote:
> >
> > > Dear Justin,
> > >
> > > Thanks very much for your reply!
> > >
> > >
> > > I guess the use of the Parrinello-Rahman barostat should not be a
> > problem
> > > because the optimization ran successfully if I turned off the morse
> > > potential. Actually, I have already done the nvt optimization
> > without morse
> > > potential before I moved to npt optimization with morse potential,  the
> > > error was the same for nvt with morse potential. I just do not know
> > why the
> > > morse potential was not working. Do you have some other ideas which may
> > > result in the problem? Thanks very much!
> > >
> >
> > Well, Morse potentials aren't the functional form with which any of the
> > biomolecular force fields in Gromacs were parametrized, so either (1)
> > there's a
> > bug that needs to be fixed or (2) you're doing something incompatible
> > and the
> > model physics is breaking down.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
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