[gmx-users] water molecules (interfacial)

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 13 15:00:34 CET 2010

atila petrosian wrote:
> Dear Justin
> are you sure g_dist -dist give me what I need. if so, how?
> since, dist.xvg gives distance vs time and lifetime.xvg gives number of 
> contact vs time. while, I want number of water molecules (interfacial) 
> to be within 2.4 A distance from both the protein and the ligand during 
> simulation. also, exact numeration of each water being in interface 
> between protein and ligand.

If you've only obtained dist.xvg, then you haven't used the -dist flag, which is 
a separate command line argument.  Please see g_dist -h.  I think g_select is 
probably the better tool, but its lack of documentation at the moment makes it 
very difficult to use.  I think g_dist will provide you a suitable alternative.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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