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

Example for how to generate and run a simulation with the All-atom model using SMOG 2 and OpenSMOG
In this example, we will add a coulomb potential between charges, plus additional non-specific effective potentials, and K+, Cl- and MG2+ ions will be added. This example will use the force field described by Wang et al, JACS, 2022 (DIO: 10.1021/jacs.2c04082)


############### 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. 
- Download the template files of Wang et al (Force Field ID: AA_ions_Wang22.v1 at https://smog-server.org/smog2/template_repo/). You will have to unzip/untar, so that you have a template directory called AA_ions_Wang22.v1.  For these steps, it is assumed that AA_ions_Wang22.v1 is in your current working directory. 
 

######### 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.
Since this set of templates uses naming conventions that are not identical to the default SMOG models, we will need to specify a mapping file.  
 
>smog_adjustPDB  \
     -i 2ci2.pdb \
     -map AA_ions_Wang22.v1/AA_ions_Wang22.v1.map \
     -removewater \
     -o 2ci2.adjusted.pdb
     

Generate your force field for the biomolecule with smog2:  
- The -t flag indicates that the template directory SBM_AA+custom+ions should be used to define the force field.
- The -OpenSMOG flag indicates that the input files should be prepared for use with OpenSMOG/OpenMM
- -center will place protein equidistant from each boundary
- -boxbuffer will set the box size so that the protein is 10nm from each boundary
 
>smog2 \
     -i 2ci2.adjusted.pdb \
     -t AA_ions_Wang22.v1 \
     -OpenSMOG \
     -dname 2ci2.OpenSMOG.AA+custom+ions \
     -center \
     -boxbuffer 10

For this system, you should receive a message indicating that the total charge is +6.

Now we need to add some ions.  The ion definitions are given in the template file AA_ions_Wang22.v1/AA_ions_Wang22.v1.ions.def.  The file gives the ion name, mass, charge, c12 and c6 parameters.

To add some ions, we will use the smog_ions tool. Here, we are going to define the ions based on the *.ions.def file in the template directory. We would like to add 2 MG2+ ions


>smog_ions \
	-t AA_ions_Wang22.v1 \
	-f 2ci2.OpenSMOG.AA+custom+ions.top \
	-g 2ci2.OpenSMOG.AA+custom+ions.gro \
	-OpenSMOG 2ci2.OpenSMOG.AA+custom+ions.xml \
	-of 2ci2.OpenSMOG.AA+custom+ions.MG.top \
	-og 2ci2.OpenSMOG.AA+custom+ions.MG.gro \
	-OpenSMOGout 2ci2.OpenSMOG.AA+custom+ions.MG.xml \
	-ionnm MG \
	-ionn 2

By adding 2 Mg2+, we bring the total charge to 10.

We will now neutralize the system with 10 Cl- ions.

>smog_ions \
	-t AA_ions_Wang22.v1 \
	-f 2ci2.OpenSMOG.AA+custom+ions.MG.top \
	-g 2ci2.OpenSMOG.AA+custom+ions.MG.gro \	
	-OpenSMOG 2ci2.OpenSMOG.AA+custom+ions.MG.xml \
	-of 2ci2.OpenSMOG.AA+custom+ions.MGCL.top \
	-og 2ci2.OpenSMOG.AA+custom+ions.MGCL.gro \
	-OpenSMOGout 2ci2.OpenSMOG.AA+custom+ions.MGCL.xml  \
	-ionnm CL \ 
	-ionn 10


#### 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+custom+ions.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+custom+ions.py