Downloads
Curriculum Vitae (PDF (English), PDF (Czech), check also the online version)
List of Publications (PDF (English), PDF (Czech), check also the information available online in the Publications section and its subsections)
Both documents can be downloaded in the LaTeX source form in a single .tar.bz2 archive.
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 forrms 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, programs, and data
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)
Fujitsu Siemens Amilo Pro V3205 Debian Etch Installation Guide - provides some information about Linux installation on this nice notebook. Xorg configuration is also included.
