RESTrain

RESTrain is a flexible tool for automating scaling in REST (Replica Exchange with Solute Tempering) molecular dynamics simulations that selectively accelerate sampling of user-chosen regions using PLUMED + GROMACS. It enables selective acceleration of conformational sampling in targeted regions—ideal for enhancing the dynamics of protein loops, binding sites, or disordered regions without globally heating the system.

🔍 Features

• Supports partial REST region definition via index files
• Compatible with GROMACS setups and topologies
• Generates .mdp files, index groups, and exchange configurations
• Includes templates for submission scripts on HPC clusters

⚙️ Requirements

• Python 3.x
• GROMACS (tested on 2019+)
• NumPy

🔧 Scripts

• partial_tempering.sh: Applies REST scaling factors (e.g., 1.0, 0.926, 0.856…) to Amber-style .top files via PLUMED.
• partial_tempering-charmm.py: Applies REST scaling factors (e.g., 1.0, 0.926, 0.856…) to Charmm-style .top files via PLUMED.

---

🚀 Example Usage

Amber-based REST:

./partial_tempering.sh 1.00   < processed_new.top > abeta16-22_amber_rest0.top
./partial_tempering.sh 0.926  < processed_new.top > abeta16-22_amber_rest1.top
./partial_tempering.sh 0.856  < processed_new.top > abeta16-22_amber_rest2.top
...