Links
Research places
Scuola Internazionale Superiore di Studi Avanzati (SISSA)
Statistical and Biological Physics Sector of SISSA
Research groups:
Prof. Elisa Molinari
Prof. Michele Parrinello
Prof. Carlos Bustamante
Prof. Paolo Carloni
Societies
Journals and databases
Journals
Proceedings of the National Academy of Sciences of the U.S.A.
Journal of the American Chemical Society
Angewandte Chemie International Edition
Journal of Chemical Theory and Computation
Reviews
Annual Reviews of Biochemistry
Current Opinion in Chemical Biology
Current Opinion in Structural Biology
Nature Reviews in Molecular Cell Biology
Trends in Biochemical Sciences
Repositories and virtual journals
Virtual Journal of Biological Physics Research
Search engines
Software
Classical molecular dynamics simulations
AMBER: a molecular dynamics package which includes a wealth of tools to generate new molecules
GROMACS: a very fast molecular dynamics package
NAMD: another molecular dynamics package, optimized for large parallel machines
DLPOLY: yet another molecular dynamics package, with very flexible force-field definition
LAMMPS: highly scalable and flexible molecular dynamics package, suitable for biological and material science applications
Ab initio calculations
Quantum-ESPRESSO: a package for ab initio calculations
SaX: a package for GW and excitonic calculations
CPMD: a code for ab initio molecular dynamics
CP2K: another code for ab initio molecular dynamics, with a very efficient basis set
Tools for molecular dynamics
PLUMED: a plugin for free energy computations
gle4md: resources on the usage of colored noise in molecular dynamics
VMD: graphical software to show and analyze molecular dynamics trajectories
RNA: secondary structure prediction
Figures, movies and presentations
Keynote (for Mac): similar to Powerpoint, but better
LaTeXiT (for Mac): trasforms LaTEX formulas to pdf, so as to include them in presentations
Asymptote: a scripting language to produce 2D vectorial graphics
Libplot: a C plotting library
Netpbm: a command line tool for image conversion and mpeg encoding
Gnuplot: basic but very flexible 2D plotting tool, every scientist should know it
Clker: collection of free clips art
Processing: a simpler java, useful to prepare movies and presentations
Word processors
Lyx: a graphical frontend for LaTeX, with a very fast equation editor
JabRef: a graphical frontend for BibTex
Pages (for Mac): similar to Word, but better - very good for posters or assembled images
OpenOffice: an open source alternative to Microsoft Office
Programming
Git: a modern distributed version control system
Cplusplus.com: resources for C++
C++ FAQ: advanced FAQ for C++ programming
Online books: a collection of online books to learn several programming languages