[gmx-users] TFE-water simulation

Justin Lemkul jalemkul at vt.edu
Thu Oct 24 19:15:50 CEST 2013

On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote:
> Dear Justin,
> I have not constructed the system but I have downloaded it from ATB
> website. To maintain the number of TFE and water molecules(1:1 v/v) in the
> system (I don't want to add extra water molecules) I tried many options in
> genbox but still it adds 678 water molecules. Can you provide me some hint?

Not without seeing your actual command(s).

> Is their need to remove periodicity of this pre-equilibrated system as in
> case of lipids?

No idea.  Are the molecules broken in the initial configuration?



Justin A. Lemkul, Ph.D.
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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