Carma v.1.1 released.

From: Nicholas M Glykos (
Date: Thu Oct 27 2011 - 12:54:24 CDT

Dear All,

It is time for my yearly (October's) unashamed 'carma' plug. Be merciful.


                               carma v.1.1

We have released a stable new version (version 1.1) 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
suitable for GNU/Linux, MacOSX (both i686 and ppc) and windows.

WHAT'S NEW : Calculation of RMSD matrices, PCA-based cluster analysis is now
based (and reports) variance explained as a function of the number of
clusters, 3D landscapes produced in CNS map format (readable by VMD),
bending angle calculation (contributed by Ian Grant), several bug fixes.
Experimental: inclusion of chi_1 angles in dihedral PCA analysis.

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 carma's mailing list at (and not, for
example, to the innocent mailing lists that I've misused for advertising
this new version).

Best regards,

          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,

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