[gmx-users] Protein ligand complex simulation

Justin Lemkul jalemkul at vt.edu
Mon Apr 3 13:51:12 CEST 2017

On 4/1/17 8:59 AM, RAHUL SURESH wrote:
> I followed the complex simulation tutorial. Minimisation for 2ns

FYI there is no time during energy minimization, so you did not do "2 ns" of 

> I used auto dock to dock ligand with protein. During simulation I find the
> ligand out of protein. Is that usual?

This is probably a periodicity effect.  There's no way during the course of 
minimization that a ligand-protein complex can completely dissociate.  Use 
trjconv to make sure you've properly re-imaged the system.  A simple recentering 
should do it.



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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