Miscellaneous

This section of the webpage does not receive any updates any longer!

Publications

If you are interested in the listing of the given type of publication, you can use the left sidebar menu items or following links for journal articles, presentations and posters, and other publications, respectively.

Research Articles, Journal Papers

I’m author or co-author of 23 papers in various scientific journals.

The links to the respective journals/papers together with complete references are given in the journal articles section of this webpage.

Lectures, Presentations, Posters

Conference and seminar presentations (both PDF document and LaTeX source are available for most of them). 6 conference talks and 9 seminar talks are currently available. LaTeX source and resulting PDF document is also available for 1 poster.

Other Publications – Theses, Books, …

This section contains my diploma and doctoral theses in PDF format. LaTeX source is also available. I also added my project report for the Classical and Quantum Molecular Dynamics course I visited in 2004 (if I recall correctly). Reference to book Physics and Chemistry of Ice is also given here (I’m author of one of the chapters).

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)