[AMBER] write PCA mode trajectory with cpptraj

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Fri, 5 Jun 2015 10:18:35 +0200

Dear all,

I would like to make a suggestion for cpptraj development ... Currently
when writing a PCA mode trajectory with the command

"runanalysis modes name ${prot1}.pev trajout ${prot1}_mode01.nc
trajoutfmt netcdf pcmin -505.87 pcmax 419.99 tmode 1"

the values for pcmin and pcmax that correspond to the trajectory
projected onto the mode have to be separately searched for. Would it be
possible to adapt cpptraj to actually automatically get these values
from the trajectory projection onto modes ? Of course one can use values
such as -1000 to 1000 but those include motion not sampled during the
trajectory and any further analysis on the mode trajectory beyond simple
visualization is meaningless.

Best wishes

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Fri Jun 05 2015 - 01:30:10 PDT
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