rem.sh script implements replica exchange simulations for all-atom model. It assumes that between replica exchanges the system is evolved using CHARMM. The script calls exchange.exe (exchange.f90 code), which performs exchanges of coordinates and velocities as well their rescaling. All neighboring replica pairs are subject to exchange. The CHARMM simulations file is dynamically generated using template file charmm_template.inp. As an example we provide charmm_template.inp for SASA and CHARMM19 implicit water simulations. Below rep is the replica number, run is a REM trajectory number, and repstep is a REM step number.
rem.sh uses the following input files:
The following output files are generated:
The following parameters determine REM simulations:
The program exchange.f90 has three parameters that must be set before REM simulations
The scripts and codes available on this page are free for non-commercial use. The users can change or modify them provided that the software is used for non-commercial purposes.