[gmx-users] g_select dynamic indices

[Justin A. Lemkul]

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

-- 
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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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