[gmx-users] trjconv fit subset of atoms

Berk Hess gmx3 at hotmail.com
Thu Feb 26 20:12:59 CET 2009


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.


To: gmx-users at gromacs.org
From: jadelman at 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.

 ------------------------------------------------------------------------------------------------------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                   jadelman at berkeley.edu------------------------------------------------------------------------------------------------------ 

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