[gmx-users] H-bonds per molecule across the box

Justin Lemkul jalemkul at vt.edu
Thu Jul 26 12:50:59 CEST 2012

On 7/26/12 6:23 AM, akn wrote:
> Dear Gromacs users,
> Is it easily possible to calculate the number of H-bonds per molecule across
> the box by using gromacs? If it is, how can I do this?

One would have to use g_select on a particular region of the box (simple 
coordinate boundaries) to work with atoms in that region.  The result is an 
index file for each frame in the trajectory.  You must then loop over all these 
index groups (which may be of different size in each frame) and conduct analysis 
using a for-loop in a shell script (or something similar) since there is no 
automatic way to use the index files produced by g_select in this case.

See the discussion on this topic from last week in the archive.



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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