[gmx-users] g_select dynamic indices

[Yao Yao]

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.

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.

thanks,

Yao



________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Yao Yao <yao0o at ymail.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, November 30, 2011 1:57 PM
Subject: Re: [gmx-users] g_select dynamic indices
 


Yao Yao wrote:
> Hi Gmxers,
> 
> I used g_dist to find all water molecules within 5 Angstrom of a protein in a trajectory with a little surprise that gromacs directly prints out those water on my screen rather than in an output file.

According to g_dist -h, that's what you should expect :)

> Since in each frame, those water molecules are not the same, I realize I need to make a dynamic index or indices for them.
> However I do not see any flag I could possibly introduce those water in g_select and then use -on flag to produce a dynamic index.

The index groups are output by g_select.  Try g_select -select "help all" for examples of how to create groups.

-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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