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 <jalem...@vt.edu>
To: Yao Yao <ya...@ymail.com>; Discussion list for GROMACS users
<gmx-users@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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
