Dmitri Klimov, Professor
School of Systems Biology
           


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Research
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Animations
Courses
BINF 690 Numerical Methods in Bioinformatics
BINF 740 Introduction to Biophysics
BINF 741 Introduction to Computer Simulations of Biomolecules
BINF 841 Research topics in biomolecular simulations

Tutorials



Replica exchange (REM) simulations

Unix shell script for running REM simulations

Notes on using rem.sh


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:

  1. charmm_template.inp is a CHARMM simulation file.
  2. RepTemp.dat contains the list of REM temperatures
  3. charm{rep}_0.rst are the initial CHARMM restart files.
  4. exchange.exe performs replica exchanges
  5. charmlist{rep} contains the node names for replica rep


The following output files are generated:

  1. energy{rep}.dat contain the potential energies extracted from standard output of CHARMM.
  2. charm{run}_{repstep}_{rep}.dcd are trajectory files stored in ./output.


The following parameters determine REM simulations:

  1. repmax is the total number of replicas
  2. repstepmax is the total number of replica exchanges (steps)
  3. runlength is the number of integration steps between replica exchanges
  4. randseed the random seed number in CHARMM trajectory
  5. natom is the number of atoms
  6. rstlength is the number of lines in CHARMM restart file


The program exchange.f90 has three parameters that must be set before REM simulations

  1. na is the number of atoms
  2. nrep is the number of replicas
  3. mseed is the random seed number for replica exchanges


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.