WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.

ABSTRACT: Given the growing interest in path sampling methods for extending the time scales of molecular dynamics (MD) simulations, there has been great interest in software tools that streamline the generation of plots for monitoring the progress of large-scale simulations. Here, we present the WEDAP Python package for simplifying the analysis of data generated from either conventional MD simulations or the weighted ensemble (WE) path sampling method, as implemented in the widely used WESTPA software package. WEDAP facilitates (i) the parsing of WE simulation data stored in highly compressed, hierarchical HDF5 files and (ii) incorporates trajectory weights from WE simulations into all generated plots. Our Python package consists of multiple user-friendly interfaces: a command-line interface, a grap

SUBMITTER: Yang DT 

PROVIDER: S-EPMC11323263 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature