REX (Replica EXchange MD) with the MMTSB-toolset

The MMTSB Toolset is a group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD (both constant temperature and replica exchange or REX) with CHARMM or AMBER. This page is specifically for the REX aspect of the toolset. Full documentation can be found here.

There are a lot of (good) tutorials around for the MMTSB toolset and I recommended that you follow at least one of these prior to setting up your own simulation. For example you can find the tutorials from the 2006 MMSTB workshop here.

Tutorials

• Installing and setting up the MMTSB toolset
• Running a REX simulation with CHARMM
• Extracting information from a REX simulation i.e. rgyr and rmsd order parameters
• Producing a free energy surface using WHAM
• Locating and extracting structures (pdbs) from a REX simulation
• Restarting a REX simulation and combining the results