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
----------------------------------------------------------------------
--------------------------------
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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