[gmx-users] em and nvt problem

[Justin Lemkul]

On 5/25/17 7:12 AM, Kashif wrote:
> Hi
> 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 ........
> step4b_n6.pdb
> step4c_n6.pdb
> step5b_n6.pdb
> step5c_n6.pdb
>
> 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 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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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