[gmx-users] sampling conformation on the basis of RMSD value

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 18 09:26:11 CEST 2008


> below you can find a "dirty" perl script that I used to extract

A dirty perl script... That's a tautology! :p

Of course, to put that remark on the list, I sort of oblige myself to
add two cents to the discussion :p I recall that the original question
was literally asking to extract the frames which fall below a certain
RMSD cut-off from a reference. That's not (necessarily) the same as
extracting the members belonging to a certain cluster. There may be
several (parts of) clusters meeting the RMSD criterium. If the purpose
is to filter based on RMSD prior to a cluster analysis, you would need
to extract those frames from the trajectory first. trjconv offers an
option -drop for that. This allows reading an .xvg file along with
your trajectory and using -dropunder x.y you can select all frames
which have a value under the one specified :)

Hope it helps.


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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