Solvate module

SolvateTask

class esteem.tasks.solvate.SolvateTask(**kwargs)

setup_amber()

Handles setup of the solvated model using AmberTools.

The setup has 5 main sections:

1. Counterions are set up
2. Amber input files for the solute molecule are created
3. Amber input files for the solvent molecule are created
4. A box of solvent is added to the solute, and counterions added
5. 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()

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()

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 and snapshots

Outputs:

A trajectory file, named ‘{solute}_{solvent}_{md_suffix}/{solute}_{solvent}_solv.traj’ which contains self.nsnaps geometries of the solvated box, each spaced by self.nsteps steps of self.timestep units of time (wrapper-dependent).

An example for catechol in water with the default md_suffix

Task Arguments

usage: __main__.py [-h] [--solute SOLUTE] [--solvent SOLVENT]
                   [--boxsize BOXSIZE] [--timestep TIMESTEP] [--temp TEMP]
                   [--nheat NHEAT] [--ndens NDENS] [--nequil NEQUIL]
                   [--nsteps NSTEPS] [--nsnaps NSNAPS]
                   [--restraints RESTRAINTS RESTRAINTS RESTRAINTS RESTRAINTS]
                   [--rest_r REST_R REST_R REST_R REST_R REST_R REST_R]
                   [--counterions COUNTERIONS] [--ewaldcut EWALDCUT]
                   [--gammaln GAMMALN] [--use_acpype USE_ACPYPE]

Named Arguments

--solute, -u	Name of solute molecule
--solvent, -v	Name of solvent molecule
--boxsize, -b	Size of simulation box for MD calculation Default: 20
--timestep, -t	Time step of Molecular Dynamics runs Default: 0.002
--temp, -T	Thermostat temperature for Molecular Dynamics runs Default: 300.0
--nheat, -H	Number of MD steps in Heating phase Default: 10000
--ndens, -D	Number of MD steps in Density Equilibration phase Default: 50000
--nequil, -E	Number of MD steps in Equilibration phase Default: 50000
--nsteps, -S	Number of MD steps between each snapshot in Snapshots phase Default: 2000
--nsnaps, -N	Number of Snapshots to save to trajectory Default: 200
--restraints, -R
	Specifies restraint atoms
--rest_r, -r	Specifies parameters for restraint
--counterions, -C
	Counterion(s) to add, eg Na Default: {}
--ewaldcut, -e	Cutoff length for Ewald calculation (See Amber manual) Default: 12.0
--gammaln, -g	Thermostat parameter: Collision frequency in ps^-1 Default: 1.0
--use_acpype, -P
	Use ACPYPE Default: False

Note: Writes the output trajectory in the format <solute>_<solvent>_solv.traj

Standalone module routines

Sets up and runs solvated Molecular Dynamics in Explicit Solvent

esteem.tasks.solvate.counterion_charge(counterions)

Calculate the net charge on the solute, given a set of counterions