**From:** Nicholas M Glykos (*glykos_at_mbg.duth.gr*)

**Date:** Mon Sep 22 2008 - 05:52:23 CDT

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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 http://www.mbg.duth.gr/~glykos/Carma.html 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).

Nicholas

-- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613 Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/

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