NAMD_CVS_Source.tar.gz_NAMD

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