[gmx-users] how many contacts has a certain atom at MD

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 21 13:01:59 CET 2011

g_mindist -on (with suitable index groups) should also do the trick.


Erik Marklund wrote:
> Or g_hbond -contact. Undfortuntely there are still issues with g_hbond 
> at the moment. Version 4.0.x seem to work better.
> XAvier Periole skrev 2011-02-21 11.37:
>> g_dist
>> On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote:
>>> Dear Gromacs Users,
>>> I would like to know if there is in gromacs an option how to 
>>> calculate how many contacts has a certain atom i(n a molecules of 
>>> interest) with water during the whole MD simulations (or at each step 
>>> of MD).
>>> Please could you advice me on this?
>>> best,
>>> Olga
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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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