[gmx-users] Re: trjconv modification

[Graham Smith]

Hi - 

I've been finding that, when dealing with several simulations of
different mutants of a protein, or a complexed and uncomplexed form,
the current indexing facilities of trjconv make it very difficult to
fit the different trajectories to the same structure file as you might
wish (e.g. fit on C-alphas, output all protein atoms).  Therefore I've
modified trjconv so that it can take two index groups, -n and -ns. -ns
then selects from the structure file and -n selects from the
trajectory and controls the output.  I've put it on the contributions
page. 

This is designed for use with -fit only, and output should be to an
xtc or trj (the res/atom fields in a pdb or gro will be wrong). The
output is often slightly different to the standard version but the
difference is always small (<= 0.005 A). 

Cheers 

Graham 

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Dr. Graham R. Smith,
Biomolecular Modelling Laboratory,
Cancer Research UK,
44 Lincoln's Inn Fields,
London WC2A 3PX,