OpenMM Molecular Dynamics module

Submodules

Module contents

OpenMM Molecular Dynamics refinement module for HADDOCK3.

The potential of OpenMM can be exploited to perform potentially different tasks, such as:

  • Run MD simulation for each model from previous step;

  • Refine the models in the middle of a docking run. For example, it can be used to refine the models coming from a [rigidbody] module before [flexref] is executed, or to replace the [mdref] step.

  • Generate conformers prior to their use in a thorough docking run.

To get a list of all possible parameters, run:

>>> haddock3-cfg -m openmm

Module workflow:

  • Generate openmm topology and fix atoms

  • Build solvation box

  • Equilibration solvation box restraining the protein

  • Run MD simulation: increase temperature, run MD, reduce temperature.

  • Either generate an ensemble of multiple frames or return the last frame.

This module will refine all models coming from the previous workflow step and send them to the next step in the workflow. If you want to use other modules such as flexref or emref after the OpenMM module, you need to recreate the topologies by simply adding a [topoaa] step in the workflow. See examples in examples/thirdparty/openmm folder.

class haddock.modules.refinement.openmm.HaddockModule(order, path, initial_params=PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/refinement/openmm/defaults.yaml'))[source]

Bases: BaseHaddockModule

HADDOCK3 OpenMM module.

classmethod confirm_installation() → None[source]

Confirm installation of openmm and pdfixer.

Raises:
create_directories() → dict[str, str][source]

Create the necessary directories and provides the paths.

name: str = 'openmm'
remove_directories() → None[source]

Remove unnecessary directories full of heavy files.

static set_max_cpu(nbcpu: int) → None[source]

Default Parameters

Easy

add_extra_particles_for_forcefield

default: False
type: boolean
title: Add extra particles for forcefield.
short description: Add extra particles for forcefield if needed such as e.g. Drude particles.
long description: Add extra particles for forcefield if needed such as e.g. Drude particles.
group: force field
explevel: easy

constraints

default: ‘HBonds’
type: string
title: Integration constraints.
choices: [‘None’, ‘HBonds’, ‘AllBonds’, ‘HAngles’]
short description: Integration constraints used to allow for larger integration time step.
long description: Integration constraints used to allow for larger integration time step. For extra info see http://docs.openmm.org/latest/userguide/application/02_running_sims.html#constraints
group: restraints
explevel: easy

explicit_solvent_model

default: ‘amber14/tip3p.xml’
type: string
title: Explicit solvent models.
choices: [‘amber14/tip3p.xml’, ‘amber14/spce.xml’, ‘charmm36/spce.xml’, ‘amber14/tip4pew.xml’, ‘charmm36/tip4pew.xml’, ‘charmm36/tip5p.xml’]
short description: Solvent models supported by the OpenMM modeller to build the water solvation box.
long description: Solvent models supported by the OpenMM modeller to build the water solvation box.
group: force field
explevel: easy

forcefield

default: ‘amber14-all.xml’
type: string
title: Forcefield used by OpenMM.
choices: [‘amber14-all.xml’, ‘amber14/protein.ff14SB.xml’, ‘amber14/protein.ff15ipq.xml’, ‘amber14/DNA.OL15.xml’, ‘amber14/DNA.bsc1.xml’, ‘amber14/RNA.OL3.xml’, ‘amber14/lipid17.xml’, ‘amber14/GLYCAM_06j-1.xml’, ‘charmm36.xml’]
short description: Forcefields that can be used by OpenMM.
long description: Forcefields that can be used by OpenMM.
group: force field
explevel: easy

generate_ensemble

default: True
type: boolean
title: Generate ensemble of configurations.
short description: Generate ensemble of configurations.
long description: If ‘true’, generates 1 single ensemble .pdb file holding various configurations; composed of the equilibrated one, all intermediates and the final one. If ‘false’, only return the last configuration obtained after ‘simulation_timesteps’ steps.
group: post processing
explevel: easy

implicit_solvent

default: False
type: boolean
title: Indicate use of implicit solvent.
short description: Indicate use of implicit solvent, avoids building a water solvation box around pdbs.
long description: Indicate use of implicit solvent, avoids building a water solvation box around pdbs.
group: force field
explevel: easy

implicit_solvent_model

default: ‘implicit/hct.xml’
type: string
title: Implicit solvent models.
choices: [‘implicit/hct.xml’, ‘implicit/obc1.xml’, ‘implicit/obc2.xml’, ‘implicit/gbn.xml’, ‘implicit/gbn2.xml’]
short description: Implicit solvent models supported by OpenMM.
long description: Implicit solvent models supported by OpenMM.
group: force field
explevel: easy

iniseed

default: 917
type: integer
title: Simulation seed.
min: 0
max: 1000000
short description: Set a pseudo-random seed for the simulation.
long description: Set a pseudo-random seed for the simulation. This defines how the initial velocities are created, but has no effect on the randomicity of the solvation box.
group: sampling
explevel: easy

ion_concentration

default: 0.15
type: float
title: Ion concentration.
min: 0
max: 5
short description: Ion concentration in Molar.
long description: Ion concentration in Molar.
group: sampling
explevel: easy

keep_solvent

default: False
type: boolean
title: Whether-or-not solvent be removed from provided structures.
short description: Whether-or-not solvent be removed from provided structures.
long description: Whether-or-not solvent be removed from provided structures. If ‘false’, all HETATM atoms will be removed.
group: post processing
explevel: easy

remove_center_of_mass_motion

default: True
type: boolean
title: Remove center of mass motion.
short description: Remove center of mass motion when overall molecular drift is detected.
long description: Remove center of mass motion when overall molecular drift is detected.
group: sampling
explevel: easy

rigid_water

default: True
type: boolean
title: Use rigid water.
short description: Use of rigid water in the simulation.
long description: Use of rigid water in the simulation. Flexible water molecules usually require a slower taken timestep by the used integrator.
group: restraints
explevel: easy

sampling_factor

default: 1
type: integer
title: Number of simulation replicas.
min: 1
max: 20
short description: Number of simulation replicas.
long description: Number of simulation replicas.
group: sampling
explevel: easy

solv_equilibration

default: True
type: boolean
title: Process the solvent equilibration phase.
short description: Process the solvent equilibration phase.
long description: Process the solvent equilibration phase. If ‘true’, the solvent will be equilibrated while constraining proteins positions to intial ones.
group: sampling
explevel: easy

temperature_kelvin

default: 298.15
type: float
title: Average temperature.
min: 1.0
max: 1000.0
short description: Average temperature used by e.g. the integrator or by for temperature coupling.
long description: Average temperature used by e.g. the integrator or by for temperature coupling.
group: sampling
explevel: easy

Expert

equilibration_timesteps

default: 2000
type: integer
title: Equilibration timesteps.
min: 0
max: 100000
short description: Equilibration timesteps performed without saving the simulation state.
long description: Equilibration timesteps performed without saving the simulation state.
group: sampling
explevel: expert

padding

default: 1.0
type: float
title: Padding value in nanometers.
min: 0.3
max: 10
short description: Padding value in nanometers.
long description: Padding value in nanometers. This is used to create the solvation box by adding water molecules around the molecule up to this padding distance. When performing a long refinement of a complex, increase this parameter as the molecules will likely move away from each other.
group: sampling
explevel: expert

ph

default: 7.4
type: float
title: pH of the buffer.
min: -3.0
max: 12
short description: pH of the buffer.
long description: pH of the buffer. This has an infulence on the protonation states of the resiudes.
group: simulation
explevel: expert

save_intermediate

default: 1
type: integer
title: Number of intermediate configurations to save.
min: 0
max: 100
short description: Number of intermediate configurations to save during the simulation.
long description: Number of intermediate configurations to save during the simulation. The code divides the length of the simulation (simulation_timesteps) by this parameter to get how often configurations should be saved.
group: sampling
explevel: expert

simulation_timesteps

default: 2000
type: integer
title: Simulation timesteps.
min: 0
max: 1000000
short description: Simulation timesteps performed during the simulation.
long description: Simulation timesteps performed during the simulation.
group: sampling
explevel: expert

solv_eq_max_temperature_kelvin

default: 310.0
type: float
title: Upper boundary of temperature to reach during solvent eauilibration phase.
min: 1
max: 400
short description: Upper boundary of temperature to reach during solvent eauilibration phase.
long description: Upper boundary of temperature to reach during solvent eauilibration phase.
group: sampling
explevel: expert

solv_eq_stepsize_fs

default: 2.0
type: float
title: Step size for the solvent equilibration phase.
min: 0.5
max: 4
short description: Step size (in femptoseconds) for the solvent equilibration phase.
long description: Step size (in femptoseconds) for the solvent equilibration phase.
group: sampling
explevel: expert

timestep_ps

default: 0.002
type: float
title: Timestep definition.
min: 0.001
max: 0.004
short description: Definition of timestep used by the integrator to progress the simulation.
long description: Definition of timestep used by the integrator to progress the simulation.
group: sampling
explevel: expert

Guru

solv_eq_spring_constant

default: 20.0
type: float
title: Spring constant (k) used to restrain protein coordinates during solvent equilibration phase.
min: 0
max: 10000
short description: Spring constant (k) used to restrain protein coordintes during solvent equilibration phase.
long description: Spring constant (k) used to restrain protein coordinates during solvent equilibration phase.
group: sampling
explevel: guru

solv_eq_timesteps

default: 500
type: integer
title: Number of timesteps to be performed during solvent equilibration phase.
min: 10
max: 50000
short description: Number of timesteps to be performed during solvent equilibration phase.
long description: Number of timesteps to be performed during solvent equilibration phase.
group: sampling
explevel: guru