On 11/1/13 5:37 AM, xiao wrote:
Dear all gromacs users,
I have run a protein-ligand simulations. However, the position of the ligand
is not reasonable after 10ns simulation. There is no problem with the force
field paramers of the ligand. I am trying to constrict the ligand move for
500ps simulation. But i do not know whether it will work. Any good idea is
appreciated :)
Usually when something misbehaves, the topology is the first likely source of
error. How have you concluded that it is suitable?
Since we don't know what you're doing (description of your protocol, or even
better, .mdp files), it could simply be that you're doing something that causes
the physical model to be wrong. Provide that information and you're more likely
to get a quick and productive response.
-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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