[gmx-users] H-bonds per molecule across the box
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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