[gmx-users] Measuring hydrogen bonding in a specific region

Alex Marshall amarsh59 at uwo.ca
Tue Jul 17 22:37:00 CEST 2012

Hi all,

I have a system that consists of two distinct reservoirs filled with
water+NaCl connected by a CNT. I want to measure the average number of
hydrogen bonds per water in each reservoir as a function of time, but
my current workflow for this is far too time-consuming to get any
significant resolution:

-Have trjconv dump frames to separate .gro files (for example, in 10ns
-use g_select to create a .ndx file with groups for the waters in
either reservoir
-run g_hbond on the .gro file with the appropriate .ndx file, record
the number of hbonds and the number of donors for each reservoir

Is there any way I could automate/improve this process? I have ten of
these simulations longer than 100 ns to analyze, and I just need more
data points than I can crank out manually.

Alex Marshall
M.Sc. Candidate
Department of Applied Mathematics
The University of Western Ontario

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