Solvate module¶
SolvateTask¶
-
class
esteem.tasks.solvate.
SolvateTask
(**kwargs)[source]¶ -
setup_amber
()[source]¶ Handles setup of the solvated model using AmberTools.
The setup has 5 main sections:
- Counterions are set up
- Amber input files for the solute molecule are created
- Amber input files for the solvent molecule are created
- A box of solvent is added to the solute, and counterions added
- Restraints are calculated for the counterions
args: namespace or class
Input variables to the routine - see listing under Command-Line usage for details
Generate with a call to solvate.make_parser()
- wrapper: class
- Wrapper to run calculations of this task
-
setup_lammps
()[source]¶ Handles setup of the solvated model for a LAMMPS calculation (also uses AmberTools)
- args: namespace or class
- input variables to the routine - see listing under Command-Line usage for details
-
run
()[source]¶ Handles running of MD on a solvated model using an MD Wrapper (currently Amber or LAMMPS).
There are five phases to the task:
Setup, Heating, Density Equilibration, Equilibration and Snapshot Generation
Constraints are turned on and off as appropriate in different phases:
SHAKE constraints on -H during heating and density equil, no constraints on -H during equil and snapshots
Counterions are restrained from coming too close to the solute
- args: namespace or class
- Argument list for the whole job, with members including:
- wrapper: namespace or class
Wrapper for running components of the job, with members including:
singlepoint
,minimise
,heatup
,densityeq
,equil
andsnapshots
- Outputs:
A trajectory file, named ‘{solute}_{solvent}_{md_suffix}/{solute}_{solvent}_solv.traj’ which contains
self.nsnaps
geometries of the solvated box, each spaced byself.nsteps
steps ofself.timestep
units of time (wrapper-dependent).An example for catechol in water with the default
md_suffix
-
Standalone module routines¶
Sets up and runs solvated Molecular Dynamics in Explicit Solvent