[gmx-users] About Diffusion of Water towards Protein in ceter of box
scvsankar_agr at yahoo.com
Thu Nov 29 16:09:27 CET 2012
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 ?
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