[gmx-users] Aout Restraint on Water oxygen atoms

Justin Lemkul 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
> ; Position restraint for each water oxygen
>   [ position_restraints ]
>      i  funct       fcx        fcy        fcz
>      1    1         0           0      1000000
> #endif
>    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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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