[gmx-users] TFE-water homogeneous system -NPT
jalemkul at vt.edu
Mon Feb 10 18:50:07 CET 2014
On 2/10/14, 12:12 PM, Archana Sonawani-Jagtap wrote:
> I am trying to perform peptide simulation using TFE-water system. I did lot
> of literature search and according carried out NVT for 32ns followed by NPT
> 10ns simulation for TFE-water system.
> I found that the TFE get accumulated in the center of the box and water
> molecules surround them. The system is no more homogeneous.
> Is this normal or something is going wrong? Any help regarding this is
It sounds to me like either the force field parameters are bad (i.e. the TFE is
too hydrophobic and just aggregates) or there could be problems with the .mdp
file. Without more information, there's nothing definitive to suggest.
Justin A. Lemkul, Ph.D.
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
More information about the gromacs.org_gmx-users