Algorithms for molecular simulations

Classroom demonstrations

Here is a small collection of demonstration programs mainly on molecular simulations. A full list can be found here.

Harmonic oscillator Potts model
2D Lennard-Jones molecular dynamics 3D Lennard-Jones molecular dynamics 3D Lennard-Jones Gibbs ensemble
PDB viewer Normal-mode analysis alpha-carbon protein model
dynamic programming for two strings dynamic programming for RNA dynamic programming for two proteins

Programming

Tips and tools on programming.

Libraries

Project Description
zcom A single header zcom.h with many commonly-used utility routines for C programming. Selected features:
  • Utilities (strings, command line and configuration files, special functions)
  • Random number generation
  • Basic algorithms in molecular simulations (thermostat, collecting histograms, computing root-mean-square deviation, etc)
  • Common matrix operations (LU decompostion, eigenvalues/eigenvectors)
  • Common statistical models (Ising, Potts, Lennard-Jones)
Details.
nauty Nauty is a graphic isomorphism program (no automorphism, yes? ) written by Brendan McKay. The aim is to check if two graphs differ only by a vertex permutation. Additionally, we provide a self-contained header nau0s.h covering essential features in the official version 2.5r9.
Details.

Researches

Project Description
distr This project tries to find an unbiased way of smoothing a noisy distribution, which is common in molecular simulations. The method is “unbiased” because it is rigorously derived, but on the downside, it also requires an additional quantity called mean force.
Details.
rpt The project tries to address the following question. Given many configurations of a complex system, can we guess what the system temperature is? The answer to the above question can also be generalized to measure a general mean force.
Details.

License

Unless noticed otherwise, the following license applies to all codes and software on this website. Note, however, some external libraries used by our codes may have more restrictive licenses.

Material presented here has absolutely no expressed or implied warranty. Any use is at your own risk. Permission to use, copy and modify material presented here for any purpose is hereby granted without restrictions.