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

Justin Lemkul jalemkul at vt.edu
Thu Nov 29 16:14:12 CET 2012

On 11/29/12 10:09 AM, vidhya sankar wrote:
> 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 ?

In what way would you restrain the lipids?  I could see some value to an initial 
z-dimension restraint, but ultimately you're going to want to allow both the 
lipids and water to move freely, otherwise you're not equilibrating very well, 
you're inhibiting the process.

> My Question  is
> Can i simultaneously use Restraint for water and Lipids in Single NVT equilibration ?

Sure, if done carefully.

> 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 ?

I have no idea what this means.



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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