Turkey Beta1 Adrenergic Receptor

Example simulation of a membrane protein using a GB, implicit solvent
with a low dielectric region to model the membrane.

WARNING: The implicit membrane GB method is still in development. It has
not been well tested.

Equilibrate the structure:
/bin/bash doRunEquMD.sh

Then run (or submit) the simulation:
/bin/bash doRunMD.sh

Edit runEquMD.py or runMD.py to change simulation parameters.
Note that this is built around a class called "Zander", which reads and
write Amber/Sander files.  If you do not give it a Sander input file,
Zander will use the Sander default values.  You can override these
by setting them in the "overrideParams" dictionary.  For example, to change
the time step size to 2 femtosecond, add (or change) the following line in
your python script:
overrideParams['stepSize'] = 2e-3 * unit.picosecond

This change should be reflected in the output file generated when you
run the simulation.