Dear Justin,
Thanks for your instant reply about my problem. I've already
finished the make_ndx part, choosing the "protein" option. But for
trjconv, how can I write the command line to have the prompt "Select
group for output"? Sorry, I'm really a beginner. Thank you!
Best,
Zhenwei
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
Sent: 2010年1月13日 0:21
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the traj modification
zh.li wrote:
> Dear all,
>
>
>
> I want to remove the water molecules in the original traj file
> (run.xtc) to save the space, so that I should use the command
“trjconv”.
> But I don’t know which sub-command I should use to realize that? Does
> anyone here know how to do it? Thank you very much.
>
You'll need an index group that defines all non-solvent atoms (easily
done with
make_ndx). Pass the index file to trjconv and simply choose your
non-solvent
group when prompted "Select group for output."
-Justin
>
>
> Zhenwei Li
>
--
========================================
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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