HTMD

What is it?

HTMD is a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyze molecular systems. HTMD is based on Python, so scientists can easily extend it to their needs. With HTMD is possible to do very complex protocols in just few lines.

In a single script, it is possible to plan an entire computational experiment, from manipulating PDBs, building, executing and analyzing simulations, computing Markov state models, kinetic rates, affinities and pathways.

Citing HTMD:

If you are using HTMD in your publications please cite following papers:

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery
S. Doerr, M. J. Harvey, Frank Noé, and G. De Fabritiis
Journal of Chemical Theory and Computation 2016 12 (4), 1845-1852

Where to start

The user guide is a good place to start playing around.

Indices and tables