HTMD. HTMD is a programmable environment to prepare, execute, visualize and analyse Molecular Dynamic simulations. It uses 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. End-user solution type Please tick one or more Non-clinical research ✔ Clinical research Clinical decision support Drug discovery ✔ Design & optimisation ✔ In silico preclinical trials ✔ In silico clinical trials Personal health forecasting Provider: Acellera Contact email: xxxxxxxxxx@xxxxxxxx.xxx Number of user organisations (list the top 5): NDA Estimated users at PM0: NDA Estimated users at PM24: >500 registered academic users; >5 commercial users Estimated users at PM36: >750 registered academic users; >8 commercial users Access mode: Source URL: xxxxx://xxx.xxxxxxxx.xxx/products/high-throughput-molecular-dynamics/ User manual: xxxxx://xxxxxxxx.xxxxxxxx.xxx/docs/latest/htmd/index.html HPC Systems: Clusters, AWS (Amazon) HPC motivation: Solve unreducible model; Do uncertainty quantification. Additional user information: Commercial sensitivity.
HTMD. HTMD (High-Throughput Molecular Dynamics) is a programmable, extensible platform written in Python. It provides a complete workspace for simulation-based discovery through molecular simulations while aiming to solve the data generation and analysis problem as well as increase reproducibility. With HTMD, we intend to integrate the whole workflow of molecular simulation-based discovery in a single environment while abstracting unnecessary technical details. This reduces preventable errors in the workflow, increases reproducibility of molecular dynamics experiments, allows for the manipulation of large amounts of simulation data (order of terabytes), and opens the way for biologists and medicinal chemists to utilize simulations while focusing on the real biological problems they are trying to solve. HTMD (xxxxx://xxx.xxxx.xxx) extends the Python programming language with functions and classes to handle molecular systems at different levels while abstracting implementation details and best-practice knowledge. Python is a scripting language that enjoys widespread usage in the scientific community and thus provides an ideal platform on which to develop and distribute HTMD. HTMD’s functionalities span from molecular structure manipulation to visualization, preparing and executing molecular simulations on different computing resources, and data analysis, including the use of Markov state models (MSMs) to identify slow events, kinetic rates, affinities, and pathways. HTMD provides the user with an integrated platform for in silico molecular simulation discovery. Its functionalities range from molecular structure manipulation to system building, docking, MD simulations, simulation management, clustering, Markov models, and adaptive sampling. HTMD can be used from any python interpreter in the form of self-executing scripts as well as interactively using ipython or jupyter notebooks. The jupyter notebooks allow a user to combine code, documentation, and figures in one document, thus integrating a whole experiment, setup, and report in a single file, which can help increase the reproducibility of experiments. Additionally, notebooks provide the possibility for full remote execution of HTMD via a server (e.g., Amazon EC2) and a browser. The HTMD software, documentation, tutorials, and examples are available at xxx.xxxx.xxx, where it can be downloaded for free by academic users. 10 A strategy for end-user engagement and community building The initial exemplar solutions ...
