Constant Extension Ensemble

Required files are available in directory apomyl/cee. In this simulation we fix the both ends of protein, using harmonic constraints, a harder constraint for one end and flat constraint for other. The protein is pulled along end to end unit vector and allowed to equillibrate for 500 ps. A tcl script is used to apply forces. Issue the command

mpirun -np 16 /usr/local/namd/namd2mpi/ myo_cee.namd > cee.log &

to run simulation for one extension. Use the shell script(multirun) to perform simulations over several extensions for protein.

 ./multirun > logfile &

.The required files are in directory multirun(Please modify the path in the script.The default option works if the help directory is in directory $HOME).The Constant Extension Ensemble can also be simulated using constraints option in namd. An example of this type of simulation is located in the directory apomyl/cee/aliter.