[gmx-users] Aout Restraint on Water oxygen atoms
jalemkul at vt.edu
Sun Feb 10 20:32:01 CET 2013
On 2/10/13 10:52 AM, vidhya sankar wrote:
> Dear Justin Thank you for your reply,
> I have set the Restraint Along the Z Axis . as follows
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> i funct fcx fcy fcz
> 1 1 0 0 1000000
> When i visualize The .gro file in VMD,
> Still The water Molecules Are Leaking in the Hydrophobic core . How to Avoid This?
> May I Decrease The fcz Value to 1000 ?
That certainly doesn't make any sense. If your stronger restraints aren't
working, why would a weaker restraint work?
If the restraints were being correctly applied, it would be impossible for the
behavior you observe. I made the original recommendation assuming the membrane
was constructed in the typical way, parallel to the x-y plane. Is this the case
with your system? In general, what I was suggesting was simply to restrain the
vertical motion of the water molecules. That usually means a z restraint. Are
you using the correct define statement in the .mdp file, and is your #ifdef in
the correct location in the topology?
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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