mstool is a multiscale simulation tool for molecular dynamics simulations. It is a Python library that backmaps a coarse-grained structure into an all-atom structure (Backmap) and reviews the resulting structure (CheckStructure). It also can relax a system via Reduced Nonbonded Energy Minimization (REM) with unphysical contacts between atoms, which normal energy minimization fails to do.

All source code is available from github.com/ksy141/mstool. Please report bugs or ask questions on the Github Issues.

When using mstool in published work, please cite the following paper:

• Siyoung Kim, Backmapping with Mapping and Isomeric Information, J. Phys. Chem. B. 2023, 127, 49, 10488.

Note

This project is under active development.

Contents

• Installation
  • Option 1. PyPi
  • Option 2. GitHub
  • Option 3. Manual
• Input
  • Structure
  • Mapping
  • Force field
• Backmap
  • Example 1. Methane
  • Example 2. Ethane
  • Example 3. trans-2-butene
  • Example 4. Martini POPC
  • Example 5. Martini bilayer
  • Example 6. Triolein
  • Example 7. Membrane Protein

Indices and tables

• Index

• Module Index

• Search Page