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.

Siyoung Kim, All-Atom Membrane Builder via Multiscale Simulation, submitted.

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
• MembraneBuilder
  • Example 1. POPC bilayer
  • Example 2. Heterogeneous bilayer
  • Example 3. Triolein
  • Example 4. Membrane Protein
  • Example 5. GPCR
  • Example 6. Sphere Membrane
  • Example 7. Sphere Protein
  • Example 8. Lipid Droplet

Indices and tables

• Index

• Module Index

• Search Page