High-throughput molecular dynamics

HTMD: High-throughput molecular dynamics

HTMD is a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyse 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 analysing simulations, computing Markov state models, kinetic rates, affinities and pathways.

HTMD has been successfully used for FBDD, for GPCR ligand binding, Antibody structural analysis and more.

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Runs everywhere

HTMD can be run on a workstation, a cluster or on the Amazon cloud trough AceCloud.


HTMD allows to prepare your MD input files from a .pdb in less than 30 seconds


HTMD is a software interface designed for Medicinal Chemistry and Computational Chemistry groups.


HTMD is compatible with ACEMD, NAMD, GROMACS and AMBER.


HTMD is open source, so you can add your own applications to it.

Professional Support

Professional-grade support from our team of expert scientists and developers is available.

More tutorials and resources


  • S. Doerr , M.J. Harvey, F. Noé ,G. De Fabritiis, HTMD: High-throughput molecular dynamics for molecular discovery, J Chem Theory Comput. 12(4), pp1845-1852 (2016)
  • N. Stanley and G. De Fabritiis, High throughput molecular dynamics for drug discovery, In Silico Pharmacology, 3:3 (2015)
  • S. Doerr and G. De Fabritiis, On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations, J. Chem. Theory Comput. 10 (5), pp 2064–2069(2014)
alejandroHTMD: High Troughput Molecular Dynamics