VMD scripts
VMD is a great program for visualization and analysis of (not only) molecular dynamics calculations. You can download it and find related information here.
ColorCoord – can be used to set user field of a residue according to number of hbonds it forms with its neighbors. It was primarily written to facilitate the analysis of ice nucleation simualations. It helps to trace down the crystallization nucleus in the liquid phase. (script, documentation)
Contact – finds contact residues between 2 selections. A contact is defined by means of a cutoff distance (script, documentation)
ResDistrib – extracts distribution of residues/atoms represented by a selection around another selection (script, documentation)
SASARes – extracts the individual SASA (solvent-accesible surface area) for every residue of a selection (script, documentation)
Other scripts and programs
pyOZ – iterative solver of the Ornstein-Zernike equation written in Python and based on the SciPy/NumPy bundle for scientific computing, released under the BSD license – the program has its own homepage
prop_conv – utility for conversion of concentrations, densities and osmotic coefficients of electrolyte solutions written in Python and released under the BSD license – the program is hosted in the Downloads section of the pyOZ homepage
SEGRMS – scripts for RMS analysis of MD trajectories based on AMBER package (use ptraj or carnal programs TGZ, 2D sample image, 3D sample image)
MD analysis tools – several tools written in C for analysis of MD trajectories (currently supports AMBER and DL_POLY, but can be easily extended). Can be used to calculate density and charge profiles, electric fields, molecular orientations, diffusion constants, hydrogen bonds, radial/pair distribution functions and some others. (source .tar.bz2, README)
Linux installation on notebooks
Fujitsu Siemens Amilo Pro V3205 Debian Etch Installation Guide – provides some information about Linux installation on this nice notebook. Xorg configuration is also included.
Dell Latitude D430 Debian Lenny Installation Guide – provides some information about Linux installation on this notebook.
