[gmx-users] About Keepbyz script for Deleting sol Molecules

[Justin Lemkul]

On 10/29/12 12:54 PM, vidhya sankar wrote:
> Dear justin Thank you For your Previous reply,
>                                                                             I am deleting The Water Molecules using keepbyz script as mailed me
>
> I want to  keep waters around the head groups of my lipid, so
> How to Choose wisely  upperz and lowerz values to my system ?
>

These are the upper and lower bounds of the membrane; generally one would choose 
some representative atom of the headgroup, like phosphorus.  It's not an exact 
science.

-Justin

-- 
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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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