Ok, I think I see what's going on now. If I have two different groups
in the ndx file, I can then select between them for the different
purposes.
Sorry for the confusion.
Josh
On Feb 26, 2009, at 2:48 PM, Tsjerk Wassenaar wrote:
Josh,
-n indicates that groups are to be read from the index file, rather
than using the standard groups. It's not related to what the group is
being used for.
Cheers,
Tsjerk
On Thu, Feb 26, 2009 at 11:34 PM, Joshua Adelman
<jadel...@berkeley.edu> wrote:
I'm using 4.0.2. There are three optional ndx flags, -n -sub -fr.
As far as
I can tell, -n defines the output group (will also set the fit
group as the
same), -sub tells you the frame numbers for cutting the trajectory
into
smaller sections and -fr also has something to do with frames. If
you don't
define an .ndx file then it will ask you for a fit group, but what
I want is
to specify a particular set of atoms (not CA, backbone, etc).
Maybe I'm just missing something simple. . . .
Josh
On Feb 26, 2009, at 11:12 AM, Berk Hess wrote:
Hi,
Which version of Gromacs are you using?
In 4.0, but I think also in 3.3, trjconv ask for both a fit and an
output
group.
Berk
________________________________
To: gmx-users@gromacs.org
From: jadel...@berkeley.edu
Date: Thu, 26 Feb 2009 10:47:38 -0800
Subject: [gmx-users] trjconv fit subset of atoms
I am trying to use trjconv to generate a new .xtc file in which
all frames
have been aligned based on a subset of atoms (e.g. I have a multi-
domain
protein and I want to align the trajectory to one of the domains).
Using a
standard .ndx file only outputs the atoms associated with the
fitted domain.
I was wondering if there is a straightforward way to do what I
describe
without having to hack trjconv?
Looking at the source for do_fit.c it looks like if I were to set
the mass
of atoms that I didn't want to use in the alignment to zero, then
it might
work, but I am generally trying to avoid having to generate a tpr
file since
I'm coming from the pdb/psf world.
Any suggestions would be appreciated.
Josh
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Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/
~jadelman
Berkeley, CA 94720 USA jadel...@berkeley.edu
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Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/
~jadelman
Berkeley, CA 94720 USA jadel...@berkeley.edu
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/
~jadelman
Berkeley, CA 94720 USA jadel...@berkeley.edu
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