[gmx-users] About Diffusion of Water towards Protein in ceter of box
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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