[gmx-users] boundwaters

Justin Lemkul jalemkul at vt.edu
Mon Jan 28 16:33:21 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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