################ DESCRIPTION ###############

Example for generating and running a simulation with the All-atom model using SMOG 2 and OpenSMOG


############### PREREQUISITES ##############

- SMOG 2 must be configured and all SMOG tools must be in your PATH.  If you are using a SMOG container, this will be satisfied.
- the alias "python" must map to a version for which the OpenSMOG libraries are available. Conda environments can be helpful to set this up. 
 

######### USING SMOG2 AND SMOG-TOOLS #######

Begin with the file 2ci2.pdb, obtained directly from RCSB. For your convenience, it is in the current directory.

Preprocess the PDB file. smog_adjustPDB will remove water molecules and recognize all valid PDB keywords. smog_adjustPDB may be applied directly to the downloaded PDB file.
 
>smog_adjustPDB -i 2ci2.pdb -o 2ci2.adjusted.pdb -removewater

Generate your force field with smog2:  
- The -AA flag indicates that the Whitford '09 all-atom model should be used.
- The -OpenSMOG flag indicates that the input files should be prepared for use with OpenSMOG/OpenMM

>smog2 -i 2ci2.adjusted.pdb -AA -OpenSMOG -dname 2ci2.OpenSMOG.AA


#### RUNNING A SIMULATION WITH OPENSMOG ####

At this point, you have all files needed to start your calculations in OpenSMOG.  Using the script run.ci2.OpenSMOG.AA.py (in this directory), you can load, energy minimize and simulate the system. See comments in .py file for explanation of settings.

>python run.ci2.OpenSMOG.AA.py