carma v.0.9

From: Nicholas M Glykos (
Date: Mon Sep 22 2008 - 05:52:23 CDT

Dear All,

An unashamed plug, be merciful:


                               carma v.0.9

We have released a stable new version (version 0.9) of 'carma' which is a
stand-alone molecular dynamics analysis tool tuned for the DCD-PSF world.
The program is free, open-source software and is immediately available for
download via The distribution
includes source code, documentation and pre-compiled executable images for
GNU/Linux and windoze. Carma can calculate the variance-covariance and
cross-correlation matrices, do a principal component analysis using both
Cartesian PCA _and_ dihedral angle PCA, do a PCA-based cluster analysis,
remove overall rotations/translations, calculate the mass-weighted radius of
gyration, calculate the average CA-CA distance map and the rmsd from it (for
the length of the trajectory), calculate the average structure and atomic
rms fluctuations, calculate distances and torsion angles between arbitrary
sets of atoms, calculate solute's entropy using both Schlitter's and
Andricioaei's formulas, allow a primitive quick view of a trajectory on a
X11-capable terminal, calculate CNS- and XPLOR-compatible density maps
representing the average distribution of selected atomic species (eg. ions
or waters), etc.

Please note that all correspondence related to carma (comments, suggestions,
bug reports, flames) should be directed to me (and not, for example, to the
innocent mailing lists that I've misused for advertising this program).


             Dr Nicholas M. Glykos, Department of Molecular 
         Biology and Genetics, Democritus University of Thrace,
   University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613
      Tel ++302551030620 (77620),

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