Running janus¶

To run janus, simply type the following in the command line: .. code-block:: python

janus input.json

Structure of an input file¶

Janus uses a JSON style input file, with separate dictionary definitions for six sections.

These are:

Section title	Description
system	parameters for specifying what type of computation is desired
qmmm	QM/MM related parameters
aqmmm	adaptive QM/MM related parameters
md	parameters related to molecular dynamics simulations
hl	parameters for the high-level computation
ll	parameters for the low-level computation

The following section details the possible keywords for each section.

System¶

Required keywords¶

system_info

Description:	Files for describing the positions and topology of the initial system
DataType:	List of strings
Values:	inpcrd and prmtop files needed for Amber files, gro and top files needed for Gromacs files

Optional keywords¶

system_info_format

Description:	Specifies the format of the files given in system_info
DataType:	String
Default:	pdb
Values:	pdb, Amber, Gromacs

run_md

Description:	Whether to run a MD simulation
DataType:	Bool
Default:	False

run_qmmm

Description:	Specifies whether to run QM/MM
DataType:	Bool
Default:	False

run_aqmmm

Description:	Specifies whether to run adaptive QM/MM
DataType:	Bool
Default:	False

aqmmm_scheme

Description:	Specifies what adaptive QM/MM approach to use
DataType:	String
Values:	ONIOM-XS, Hot-Spot, PAP, SAP, DAS
Default:	None

ll_program

Description:	Specifies what program to use for the lower level computation
DataType:	String
Values:	OpenMM
Default:	OpenMM

hl_program

Description:	Specifies what program to use for the high level computations
DataType:	String
Values:	OpenMM, Psi4
Default:	Psi4

md_simulation_program

Description:	Specifies what program to use for MD simulation
DataType:	String
Values:	OpenMM
Default:	OpenMM

md_restart

Description:	Whether to restart a simulation from saved checkpoints
DataType:	Bool
Default:	False

md_restart_checkpoint_filename

Description:	Name of checkpoint file to read for restart
DataType:	String
Default:	checkpoint.chk

md_restart_forces_filename

Description:	Name of force file to read for restart
DataType:	String
Default:	forces.pkl

QMMM¶

Required keywords¶

qm_atoms

Description:	Specifies what atoms to treat with QM (or other high level treatment)
DataType:	List
Notes:	If run_aqmmm is true, the qm_atoms is the same as the qm_center

Optional keywords¶

embedding_method

Description:	Specifies what QM/MM embedding method to use
DataType:	String
Values:	Electrostatic, Mechanical
Default:	Mechanical

qmmm_scheme

Description:	Specifies what energy scheme to use for computing the QM/MM energy
DataType:	String
Values:	subtractive
Default:	subtractive

boundary_treatment

Description:	Specifies the scheme to use for the treatment of dangling bonds
DataType:	String
Values:	link_atom, RC, RCD
Default:	link_atom

link_atom_element

Description:	Specifies what atom to use for the link atom
DataType:	String
Values:	H
Default:	H

AQMMM¶

Required keywords¶

qm_center

Description:	Specifies what atoms to designate as the center for the high level treatment
DataType:	List

Optional keywords¶

partition_scheme

Description:	Specifies how to define the buffer zone atoms
DataType:	String
Values:	distance
Default:	distance

Rmin

Description:	Specifies the radius from the qm center to the inner boundary of the buffer zone in distance partitioning in angstroms
DataType:	Float
Default:	3.8

Rmin

Description:	Specifies the radius from the qm center to the outer boundary of the buffer zone in distance partitioning in angstroms
DataType:	Float
Default:	4.5

modified_variant

Description:	Specifies whether to use the modified variant of either the PAP or SAP schemes
DataType:	Bool
Default:	False

Molecular Dynamics¶

Required keywords¶

start_qmmm

Description:	Specifies at which step to start the QM/MM or adaptive QM/MM approach
DataType:	Int
Notes:	QM/MM can be started after taking some MD steps so the system can equilibrate

end_qmmm

Description:	Specifies how many
DataType:	Int
Notes:	end_qmmm - start_qmmm = total number of MD steps that will use QM/MM forces

Optional keywords¶

step_size

Description:	The step size of the MD simulation in femtoseconds
DataType:	Int
Default:	1

md_ensemble

Description:	Ensemble of MD simulation
DataType:	String or List of Strings
Values:	NVT, NVE
Default:	NVE
Notes:	If more than one ensemble is desired (i.e., NVT run before NVE) a list can be created in the order of what is run

md_steps

Description:	Specifies how many total steps to take for the MD simulation
DataType:	Int or List of Ints
Default:	end_qmmm
Notes:	If more than one md_ensemble is desired, the steps for each can be specified in a list where each element will correspond to the steps run in each ensemble specified in md_ensemble. The step number specified with start_qmmm will be taken as the step number of the last ensemble specified at which to start QM/MM

return_trajectory_interval

Description:	Whether to return the trajectory of the MD simulation. Keyword value lists the frame interval to save.
DataType:	Int
Default:	0 (trajectory not returned)

return_trajectory_filename

Description:	name of trajectory file to return
Datatype:	String
Default:	output

trajectory_format

Description:	The format of the trajectory file to return
DataType:	String
Values:	NetCDF,
Default:	NetCDF

return_system

Description:	Whether to return the final position and topology of the system in a pdb file
DataType:	Bool
Default:	False

return_system_filename

Description:	name of system file to return
Datatype:	String
Default:	final.pdb

return_info

Description:	Whether to return system information such as energy and temperature
DataType:	List of strings with values to return, will be returned in file “info.dat”
Values:	potentialEnergy, kineticEnergy, totalEnergy, temperature, density
Default:	[]

return_info_interval

Description:	The frame interval for saving energy, etc. information.
DataType:	Int
Default:	0 (info not returned)

return_info_filename

Description:	name of info file to return
Datatype:	String
Default:	info.dat

return_checkpoint_interval

Description:	Interval for forces
DataType:	Int
Default:	0

return_checkpoint_filename

Description:	Name of checkpoint file to return
DataType:	String
Default:	checkpoint.chk

return_forces_interval

Description:	Interval to return forces at
DataType:	Int
Default:	same as return_checkpoint_interval

return_forces_filename

Description:	Name of force file to return
DataType:	String
Default:	forces.pkl

High Level¶

Low Level¶

Examples¶

A input file might look like the following:

{
"system" : {
            "system_info" : "water.pdb",
            "run_aqmmm" : true,
            "run_md" : true,
            "aqmmm_scheme" : "ONIOM-XS",
            "ll_program" : "OpenMM",
            "hl_program" : "Psi4",
            "md_simulation_program" : "OpenMM"
        },

"aqmmm"  : {
            "qm_center" : [0,1,2]
        },

"md"     : {
            "start_qmmm" : 10000,
            "end_qmmm" : 12000,
            "md_ensemble" : "NVE"
        }

}

Supported codes¶

Janus only supports Psi4 for quantum mechanics computations and OpenMM for molecular mechanics and molecular dynamics.