[gmx-users] MD simullations with Morse potential

[fantasticqhl]

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
>
> -- 
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>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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