On 10/29/13 5:46 PM, larif sofiene wrote:
Greeting
I'm working on a MD of a ligand-protein complex during 40 ns
i want to analyses ligand-protein interaction hydrogen bonds
My first question :
Should i analyses a minimized frame from clustering of the trajectory
or should i analyses hydrogen bond occupancy over trajectory ?
I would think that a time average is much more useful than any single frame.
My second question :
Is it more correct if i do my analysis over the equilibrated phase of MD
(based on RMSD, radius of gyration , etc ...) for example the last 10 ns,
than doing it over the whole trajectory (40 ns) ?.
Allowing for equilibration time is generally a good idea.
-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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