rmcgibbo/openmm-cmd — pull request #23 by leeping (2013-11-05 13:18:06+00:00)
Title: Sysxml

This fix should print out the correct traits to the terminal and config file when deserializing an XML.

```
leeping@not0rious:~/src/openmm-cmd/examples/03-ExamplePDB-SysXML$ openmm --coords input.pdb --sysxml system.xml | tee openmm.out
>>> ###################################################################
>>> # To use this script, paste all of the lines starting with the
>>> # three less than signs (>>>) into a python interpreter.
>>> ###################################################################
>>>
>>> from simtk.unit import *
>>> from simtk import openmm as mm
>>> from simtk.openmm import app
>>>
>>> pdb = app.PDBFile('input.pdb')
>>> topology = pdb.topology
>>> positions = pdb.positions
>>> system = XmlSerializer.deserializeSystem(open(system.xml).read())
>>> integrator = mm.LangevinIntegrator(300*kelvin, 1.0/picosecond, 2*femtosecond)
>>> platform = mm.Platform.getPlatformByName('CUDA')
>>> platformProperties = {'CudaPrecision': 'mixed'}
########################################################################
# Option Summary. A more detailed config file is saved to config.out.ini
########################################################################

[General]
platform = CUDA # default value
coords = input.pdb # your selection
precision = Mixed # default value
sysxml = system.xml # your selection

[System]

[Dynamics]
integrator = Langevin # default value
dt = 2*femtosecond # default value
temp = 300*kelvin # default value
collision_rate = 1.0/picosecond # default value

[Simulation]
n_steps = 10000 # default value
restart_file = restart.json.bz2 # default value
minimize = True # default value
restart_freq = 5000 # default value
traj_file = output.dcd # default value
read_restart = False # default value
progress_freq = 1000 # default value
write_restart = True # default value
traj_freq = 1000 # default value

```