From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Mon Oct 27 2014 - 06:09:24 CDT
It is time for my yearly unashamed 'carma' plug. Be merciful.
We have released a stable new version (version 1.4) 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 and windows for carma, grcarma (the carma
graphical user interface) and cluster5D (a program to perform 5D PCA-based
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), calculate RMSD matrices, export 3D PCA-based landscapes in CNS
map format (suitable for direct input to VMD), calculate fraction of native
contacts using three different Q implementations, etc.
grcarma is a graphical user interface that fully automates several of the
most common analysis tasks ranging from automated dPCA-cPCA-based clustering
(with automatic extraction of representative structures), to secondary
structure analysis, calculation of RMSD matrices, and convergence analysis
using Good-Turing statistics.
This release also includes 'cluster5D', a program to automatically perform
five-dimensional PCA-based clustering of molecular dynamics trajectories.
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).
-- 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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