On 2/10/14, 12:12 PM, Archana Sonawani-Jagtap wrote:
Hello, 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 appreciated.
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 -- ================================================== 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 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
