From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Tue Oct 06 2009 - 06:47:09 CDT
Hi Anirban,
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).
Josh
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 &
> DCD
> files.
>
> Nicholas
>
>
> ˛ 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)
> +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:20 CST