On 9/1/13 11:36 AM, Albert wrote:
Hello:
I've finished a MD with Gromacs and I found that the water molecules inside
certain region of my protein is very flexible: the movement of them are very
fast; in other region there are very stable. I am just wondering is there any
tool in Gromacs can differentiate the water molecules' flexibility?
Maybe g_msd or g_rmsf, but I don't think there's anything specifically designed
to address water molecules, and the term "flexibility" can have far too many
meanings ;)
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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