[gmx-users] About Diffusion of Water towards Protein in ceter of box

vidhya sankar scvsankar_agr at yahoo.com
Thu Nov 29 16:09:27 CET 2012

Dear Justin,
                   Thank you for your Previous Reply 

To avoid the Diffusion of Water You Suggested  me s follows

The better approach would be a position restrain along the z-axis only, allowing 
the lipids to perhaps re-orient and pack a bit better, followed by NVT 
equilibration in the absence of any restraints on water. 

According to your Suggestion Should i Do the Two times Equilibration With restraint On water only in First NVT equilibration followed by another NVT equilibration without restraint on Water But Only With Lipids ?

My Question  is 

Can i simultaneously use Restraint for water and Lipids in Single NVT equilibration ?

If i can 

My NVT equilibration is Successful  (means No Diffusion of Water in the Tail Part.)
But After That When I do NPT Equilibration  There is Diffusion Of Some Water molecules Towards the protein in the center of box  Not towards Tail of Lipids
Is this Behavior is ODD or Normal ?
If it is ODD May I again use the Restraint on Water During NPT Equilibration ? or May I continue the MD ?

Thanks Advance

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