HTMD, developed by the team of Prof. Gianni de Fabritiis at the Universitat Pompeu Fabra (ES), is a programmable environment to prepare, execute, visualize and analyse Molecular Dynamic simulations in HPC or HTC systems, including AWS. It is a Python-based programmable environment to perform system preparation and building, execution of simulations with different MD codes using adaptive sampling schemes and generate Markov State models to analyse simulations. The code is now maintained by Acellera; it is distributed commercially, but it remains free for academic users.
Non-clinical research; Drug Discovery; Drug Design & hit to lead optimisation.
Solve unreducible model; Do uncertainty quantification.
- HTMD official website
- HTMD GitHub
- HTMD documentation
- Accellera Youtube channel
- CompBioMed webinar: High Throughput Molecular Dynamics for Drug Discovery
- High Throughput Molecular Dynamics Simulations for Drug Discovery
- S. Doerr, MJ. Harvey, F. Noé and G. De Fabritiis. J. Chem. Theory Comput. (2016) 12 (4), pp 1845-1852.
- S. Doerr and G. De Fabritiis. J. Chem. Theory Comput. (2014) 10 (5), pp 2064–2069.
- G. Pérez-Hernández, F. Paul, T. Giorgino, G. De Fabritiis, F. Noé., J Chem Phys (2013) Jul 7;139(1):015102.