[gmx-users] trjconv fit subset of atoms

[Joshua Adelman]

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                   jadelman at berkeley.edu
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