
This directory contains Tcl scripts that implement replica exchange
for NAMD, using a Tcl server and socket connections to drive a
separate NAMD process for every replica used in the simulation.
Replica exchanges and energies are recorded in the potenergy.dat,
realtemp.dat, and targtemp.dat files written in the output directory.
These can be viewed with, e.g., "xmgrace -nxy ....potenergy.dat"
There is also a script to load the output into VMD and color each
frame according to target temperature.  An example simulation folds
a 66-atom model of a deca-alanine helix in about 10 ns.

replica_exchange.tcl - master script for replica exchange simulations
  to run: tclsh ../replica_exchange.tcl fold_alanin.conf
          tclsh ../replica_exchange.tcl restart_1.conf
  uses:
    namd_replica_server.tcl - general script for driving NAMD slaves
    spawn_namd.tcl - variety of methods for launching NAMD slaves

show_replicas.vmd - script for loading replicas into VMD, first source
    the replica exchange conf file and then this script, repeat for
    restart conf file or for example just do vmd -e load_all.vmd

clone_reps.vmd - provides "clone_reps" commmand to copy graphical
  representation from top molecule to all others

example subdirectory:

alanin_base.namd - basic config options for NAMD
alanin.params - parameters
alanin.psf - structure
unfolded.pdb - initial coordinates
alanin.pdb - folded structure for fitting in show_replicas.vmd

fold_alanin.conf - config file for replica_exchange.tcl script
restart_1.conf - config file to continue alanin folding another 10 ns

load_all.vmd - load all output into VMD and color by target temperature

