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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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