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. AdelmanBiophysics Graduate Group Lab: 510.643.2159218 Wellman
Hall Fax: 510.642.7428University of California,
Berkeley http://nature.berkeley.edu/~jadelmanBerkeley, CA 94720 USA
jadel...@berkeley.edu------------------------------------------------------------------------------------------------------
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