On 5/16/12 5:54 AM, Steven Neumann wrote:
Dear Gmx Users,
I would like to run energy minimization with some atoms restrained - this is a
surface made of atoms which do not share any bonds. So the EM of water only. I
tries to use define = -DPOSRES
in my EM file but then the surface atoms change their positions. Thus, when I
want to run NVT equilibration I got errors of water molecules which cannot be
settled so EM is needed. Would you advise something?
Restraints do not guarantee that atoms won't move. They are simply a biasing
force that disfavors motion. Either apply a stronger force constant for the
restraints or use freezegrps to fix the atomic positions.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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