The wq_replica_exchange program runs the replica exchange molecular dynamics
simulations using the Work Queue framework. It uses the ProtoMol simulation
engine as the computation kernel.

The directory includes files for the WW protein as a test input.

To run:

1. Install CCTools.
2. Install ProtoMol and make sure its installation is in PATH.
3. ./wq_replica_exchange ww_exteq_nowater1.pdb ww_exteq_nowater1.psf par_all27_prot_lipid.inp  300 400  30
This runs the replica exchange simulations on the WW protein with 30 replicas
using temperatures between 300 and 400F.
4. Start workers:
work_queue_workers -d all <HOSTNAME> <PORT>
where <HOSTNAME> is the name of the host on which the manager is running
	  <PORT> is the port number on which the manager is listening.

Alternatively, you can also specify a project name for the manager and use that
to start workers:

1. ./wq_replica_exchange -N REPEXCH ww_exteq_nowater1.pdb ww_exteq_nowater1.psf par_all27_prot_lipid.inp  300 400  30
2. work_queue_worker -d all -N REPEXCH

For listing the command-line options, do:
./wq_replica_exchange -h

When the application completes, you will find all the output files in the
simfiles directory (or the directory specified in the -p option).
