Hi,
On Fri, Jun 5, 2015 at 2:18 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
> 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
>
Currently not directly. The issue is that in order to know the range for
'modes trajout' one needs to calculate the projections along those
eigenvectors, which requires the original coordinates used to calculate the
covariance matrix. You could probably script something up pretty easily
though. You can use the 'avg' analysis command to calculate the min and max
values of the projection data sets, which you can then use for 'modes
trajout' (this is what I currently do).
-Dan
> 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
> Vlad
>
> --
> 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
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jun 05 2015 - 13:30:04 PDT
