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

**Date:** Thu Oct 27 2011 - 12:54:24 CDT

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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 http://utopia.duth.gr/~glykos/Carma.html 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

http://groups.google.com/group/carma-molecular-dynamics (and not, for

example, to the innocent mailing lists that I've misused for advertising

this new version).

Best regards,

Nicholas

-- 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/

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