[gmx-users] TFE-water simulation
jalemkul at vt.edu
Wed Oct 23 13:56:00 CEST 2013
On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote:
> Hi all,
> I have never performed TFE-water simulation therfore I want to know after
> inserting the peptide in the pre-equilibrated TFE-water mixture, do we need
> to adjust the number of TFE or water molecules ?
That depends on how you constructed the system. genbox will not automatically
update the number of TFE, but it can update the number of water molecules if you
chose the proper command-line option. Regardless, the [molecules] section of
the .top must accurately reflect the contents of the configuration in terms of
order and number of molecules. Simple grep statements will let you count how
many of each are present.
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
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