Yao Yao wrote:
Hi Justin,
Thanks for your hints. I feel the string in g_select is pretty much like
tck/tl in VMD.
However I have not figured out the way to select a customized group
defined in .ndx file.
There's one example in the help text that is almost exactly what you want, is it
not?
All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):
"Close to protein" resname LIG and within 0.5 of group "Protein"
And one more question I have, maybe more general, if I have, say, 100
frames, g_select will give me 100 dynamic indices in the .ndx file,
I am wondering if there is a way (might be some script) that can help me
choose automatically for further processing, like g_hbond, and then I
can program to collect all frames and average them.
In other words, there many commands in gromacs that require users to
"Select a group", I am wondering if I can make this "choice" in a script
rather than when I see the prompt.
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
You'll have to analyze each frame individually, and then post-process your
output to get the averages.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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