[gmx-users] About Restraint -NPT Equlibration

Justin Lemkul jalemkul at vt.edu
Wed Feb 20 16:08:37 CET 2013

On 2/20/13 9:03 AM, vidhya sankar wrote:
> Dear Justin,
>                  Thank you for your Previous reply.
>   I am  Doing    Protein- Lipid  Simulation  For My Assembly Of Cyclic Peptide As you Told Me I  Have Used The Restraint on water oxygen Atom  Along the Z-direction for My NVT equilibration There is No Leakage of water to Hydrophobic part of Lipids  O. K
> But When I  am continuing NPT Equilibration The Water Molecules are Started to Diffuse Slightly  to Hydrophobic Part  My question is
> May I Again use Water Restraint for NPT equilibration? to avoid this Water Diffusion

Restraints during NPT on the water may not be stable.  It shouldn't require this 
level of effort to keep water molecules from leaking into the membrane.  Note 
that some water in the membrane is fine, e.g. around the ester region.  Anything 
further may be problematic but with enough time the waters will probably find 
their way out again.  If you still have lots of void space even after NVT, it 
probably indicates that the initial configuration was constructed poorly.



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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