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

Justin Lemkul jalemkul at vt.edu
Tue Jul 17 22:42:19 CEST 2012

On 7/17/12 4:37 PM, Alex Marshall wrote:
> 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
> increments)
> -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.

g_select allows you to create dynamic indices.  The resulting index file cannot 
be used automatically by any tool, but it will give you a list of all atoms that 
satisfy whatever criteria you specify (e.g. within certain coordinate ranges 
that indicate the reservoirs).  One run through the trajectory will generate all 
the index groups, then a shell script can be used to loop through all of the 
index groups (one per frame) with tools like g_hbond.



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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