[gmx-users] Unstable system [was: (no subject)]

[Justin Lemkul]

On 10/15/14 12:35 PM, Padmani Sandhu wrote:
> Hello Justin,
>
>
>
> Epot = -3.4264112e+07
> Fmax= 8.5767386e+02
> from energy minimization.
>

Seems reasonable.

> I am using force field Gromos43a1 and ligand parameters were derived from
> PRODRG.

PRODRG produces topologies full of errors.  Have you done any manual adjustments 
to improve the quality of the topology?

> I have also minimized same protein-ligand complex in the water ealier.
>

So minimization works, but does an MD simulation work?  That will help sort out 
whether or not the issue is related to the membrane.

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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