StreaMD: the toolkit for high-throughput molecular dynamics simulations.

ABSTRACT: Molecular dynamics simulations serve as a prevalent approach for investigating the dynamic behaviour of proteins and protein-ligand complexes. Due to its versatility and speed, GROMACS stands out as a commonly utilized software platform for executing molecular dynamics simulations. However, its effective utilization requires substantial expertise in configuring, executing, and interpreting molecular dynamics trajectories. Existing automation tools are constrained in their capability to conduct simulations for large sets of compounds with minimal user intervention, or in their ability to distribute simulations across multiple servers. To address these challenges, we developed a Python-based tool that streamlines all phases of molecular dynamics simulations, encompassing preparation, executi

SUBMITTER: Ivanova A 

PROVIDER: S-EPMC11539841 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature