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:

  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()[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 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

Standalone module routines

Sets up and runs solvated Molecular Dynamics in Explicit Solvent

esteem.tasks.solvate.counterion_charge(counterions)[source]

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

Command-line usage