[gmx-users] boundwaters

[Justin Lemkul]

On 1/28/13 10:02 AM, shahid nayeem wrote:
> Dear Users
> I am interested in knowing only the  water molecules which remains
> bounded to the protein during MD. Using g_select I can make a
> boundwater.ndx file which gives water molecules within a specified
> distance from the protein but it gives different water molecule from
> each snapshot. Now I want onle those water which is common in all
> frames. How to proceed from here and is there any other way to do
> this. Please help.

You should be able to write a simple script that runs through each group, stores 
the atom numbers, and then checks which ones are common to all frames.

-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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