[gmx-users] Minimization with DPOSRE

[Justin A. Lemkul]

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

-- 
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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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