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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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