[gmx-users] em and nvt problem
jalemkul at vt.edu
Thu May 25 20:58:49 CEST 2017
On 5/25/17 7:12 AM, Kashif wrote:
> Whenever I tried to simulate one of my docked complex, the energy
> minimization step converged very fast and complete at 112 steps. And when I
> proceed with NVT equilibration I got split structures like ........
> I have already docked the drug with my protein using different tool in
> order to get different docked pose of drug. So that I could get different
> topology file and coordinate file of the drug from PRODRG server.
PRODRG generates topologies that are of insufficient quality for MD simulations,
unless you significantly refine them. Use better tools like ATB or another
force field that has robust parametrization tools or easy-to-follow protocols.
Your system isn't stable, and I'd look at the ligand topology as the source of
that instability, but do follow
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
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