[gmx-users] MD simullations with Morse potential

[Tsjerk Wassenaar]

Hi Qinghua,

Can you run NVT equilibration? Does it work with nstlist set to 1?

Cheers,

Tsjerk
On Apr 26, 2014 12:29 AM, "Justin Lemkul" <jalemkul at vt.edu> 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
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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