From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Tue Oct 06 2009 - 06:47:09 CDT
Another fairly simple solution is to convert your trajectory files
from .dcd to .trr format using catdcd, and then analyze them using the
gromacs tools (g_covar, g_anaeig).
On Oct 6, 2009, at 4:47 AM, Nicholas M Glykos wrote:
>> I have run a MD simulation of a protein using NAMD. Now I want to
>> do PCA
>> (Principle Component Analysis) of it.
> Carma˛ can do both cartesian & dihedral PCA straight from your PSF &
> ˛ http://utopia.duth.gr/~glykos/Carma.html
> Dr Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office)
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
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