ProtoCaller.Protocol package¶

Here the user can find the Protocol class, which is designed to be a general bundle of an arbitrarily large set of molecular dynamics parameters used for simulations. The API has been designed to be general and interconvertible between packages. However, only GROMACS .mdp files can be currently output. This will be addressed in future versions of ProtoCaller.

Module contents¶

class ProtoCaller.Protocol.Protocol(use_preset=None, extra_params=None, **kwargs)¶

Bases: object

A wrapper for different simulation parameters.

Parameters

use_preset (str, None) – Which default preset to use. Allowed values: “minimisation”, “equilibration_nvt”, “equilibration_npt”, “production” “vacuum”.
extra_params (dict) – Used to set custom attributes with illegal Python characters in them.
kwargs – Used to set any of the attributes, custom or not.

integrator¶

Which integrator to use. Allowed values: “leapfrog”, “velocity_verlet”, “steep”, “l-bfgs”, “stochastic”.

Type: string

timestep¶

What timestep to use in ps.

Type: float

n_steps¶

How many timesteps to run the simulation for.

Type: int

skip_positions¶

How many timesteps to skip when writing the positions.

Type: int

skip_velocities¶

How many timesteps to skip when writing the velocities.

Type: int

skip_forces¶

How many timesteps to skip when writing the forces.

Type: int

skip_energies¶

How many timesteps to skip when writing the energies.

Type: int

periodic_boundary_conditions¶

Whether and how to implement periodic boundary conditions.

Type: string

neighbour_cutoff¶

Cutoff in nm for neighbour list.

Type: float

neighbour_frequency¶

How often to update the neighbour list in timesteps.

Type: int

coulomb_type¶

What type of Coulomb interactions to use. Allowed values: “cutoff”, “ewald”, “pme”.

Type: string

pme_order¶

What order of PME to use. Ignored if coulomb_type is not PME.

Type: int

coulomb_cutoff¶

Cutoff in nm for electrostatics.

Type: float

vdw_type¶

What type of van der Waals interactions to use. Allowed values: “cutoff”, “pme”.

Type: string

vdw_corr¶

What type of long-distance correction to apply. Allowed values: “no”, “energy”, “energy_pressure”.

Type: string

vdw_cutoff¶

Cutoff in nm for van der Waals interactions.

Type: float

thermostat¶

What thermostat to use. Allowed values: “no”, “berendsen”, “nose-hoover”, “andersen”.

Type: string

temp_frequency¶

Thermostat friction coefficient / collision frequency in THz.

Type: int

temp_time_coupling¶

Time constant for thermostat coupling in ps. -1 means no coupling.

Type: float

temperature¶

Simulation temperature.

Type: int

temp_groups¶

Which parts of the system to heat up. Allowed values: “all”.

Type: string

barostat¶

What barostat to use. Allowed values: “no”, “berendsen”, “parrinello-rahman”, “mttk”.

Type: string

pres_frequency¶

Barostat friction coefficient / collision frequency in THz.

Type: int

pres_time_coupling¶

Time constant for barostat coupling in ps. -1 means no coupling.

Type: float

pressure¶

Simulation pressure.

Type: float

compressibility¶

System compressibility.

Type: float

random_velocities¶

Whether to generate random velocities.

Type: bool

random_velocities_temperature¶

Temperature to sample velocities from.

Type: int

random_velocities_seed¶

Seed for random velocity sampling. -1 is random seed.

Type: int

constraint¶

Which constraints to apply. Allowed values: “no”, “h_bonds”, “h_angles”, “all_bonds”, “all_angles”.

Type: string

constraint_type¶

Which constraint algorithm to use. Allowed values: “lincs”, “shake”.

Type: string

free_energy¶

Whether this is a free energy calculation.

Type: bool

current_lambda¶

The current lambda. Indices start from 0.

Type: int

coulomb_lambdas¶

Initialises coulomb_lambdas.

Type: [float]

vdw_lambdas¶

Initialises vdw_lambdas.

Type: [float]

bonded_lambdas¶

Initialises bonded_lambdas.

Type: [float]

restraint_lambdas¶

Initialises restraint_lambdas.

Type: [float]

mass_lambdas¶

Initialises mass_lambdas.

Type: [float]

temperature_lambdas¶

Initialises temperature_lambdas.

Type: [float]

write_derivatives¶

Whether to write dH/dλ.

Type: bool

softcore_vdw¶

Apply soft-core potential to van der Waals interactions.

Type: bool

softcore_coulomb¶

Apply soft-core potential to Coulomb interactions.

Type: bool

softcore_alpha¶

Soft-core alpha parameter, default is 0.5.

Type: float

softcore_lambda_power¶

Power for lambda in the soft-core function.

Type: int

write(engine, filebase='protocol')¶

Writes the protocol to a file for a specific MD engine.

Parameters

engine (str) – Determines the format of the file. Allowed values: “GROMACS”.
filebase (str, optional) – The base of the output file.

Returns

filename – The absolute path to the output parameter file.

Return type

str