[gmx-users] protein-ligand complex by gromacs

Justin Lemkul jalemkul at vt.edu
Mon Sep 8 19:12:13 CEST 2014

On 9/8/14 12:30 PM, Mahboobeh Eslami wrote:
> hi GMX users
> i have simulated the protein-ligand complex by gromacs. I've repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box.
> I've checked all of the input files and the steps , but I did not understand why this happened.

This sounds like a simple periodicity issue.  Check your use of trjconv.



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


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