- PLUMED 2.7+
- GROMACS 2018+
- WESTPA 2.0
This repository shows how to calculate the progress coordinate of the weighted ensemble (WE) simulation using the popular molecular dynamics plugin PLUMED. The WESTPA software, capable of performing WE simulation, is integrated with PLUMED in the PLUMED-WESTPA toolbox which is demonstrated in this work with an example of a simple model of NaCl association. Two simple approaches are shown here, namely on-the-fly and post-analysis protocols, which are used to compute collective variables for weighted ensemble with PLUMED. It opens up the possibility of using complex collective variables implemented in PLUMED for propagating weighted ensemble trajectories, and potentially extend the applicability and usefulness of the WE to a significant extent.
Please check the PDF file included in the repository
Dhiman Ray University of California Irvine, USA Email: [email protected]