On 7/17/12 4:57 PM, Andrew DeYoung wrote:
Hi Justin,
I am just curious, do you have experience writing such a shell script to
iterate over the index files (one per frame)? I am just curious, because I
have been trying this, and I have found it very difficult to do using bash.
Do you use a different shell language?
Also, I wonder if anyone has ever posted such a shell script on this list.
When I look through the archives, I don't see one, but I could be wrong.
Assume we have 100 groups of arbitrary size and a fixed group (index group 0) in
the index file to which we wish to calculate hydrogen bonds. Then assume we
have 100 separate files (from trjconv -sep or whatever else) numbered
sequentially, i.e. conf1.gro, conf2.gro...conf100.gro. A simple bash script
that runs through the index groups corresponding to each of these coordinate
files would be something like:
#!/bin/bash
for i in {1..100}
do
echo 0 $i | g_hbond -s topol.tpr -f conf$i.gro -n index.ndx
done
-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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