[gmx-users] NVT problem

Justin Lemkul jalemkul at vt.edu
Sat Mar 15 20:42:53 CET 2014

On 3/15/14, 3:37 PM, Andres Ortega Guerrero wrote:
> Thank you Justin for Your Help, and advice, i have already the modification on the nvt.mdp that you suggest,  but the problem is still there, my system has about 150.000 atoms , and for the energy minization i used DFLEXIBLE, and  emtol was ajusted to 1000, i take a look to the steep0.pdb that gromacs produce, and there are atoms out of the box, but the DOX molecule is OK
> what would you suggest?
> - a emtol lower?
> - a water and dox md? ( maybe the DOX.itp can be the problem) ?

Several ideas/questions:

1. Does energy minimization complete adequately?  Can it proceed further (lower 
emtol than 1000)?
2. If you have used flexible water, you should re-minimize with 
constraints/rigid water.  It is common that a minimized system has badly 
distorted the geometry of one or more water molecules.
3. "Out of the box" is not an issue if you are using PBC, because no such thing 
exists.  If something has gone flying out of the rendered unit cell (i.e. large 
coordinates), that suggests severe instability of the initial configuration and 
would be a likely source of the problem.
4. What force field are you using?
5. What is the source of your DOX.itp parameters?  What is DOX?



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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