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BioSpring Simulation Parameter File (.msp file)

Introduction

The BioSpring simulation parameter file describes the parameters and settings of the simulation. Its extension is .msp.

The syntax is:

[Setting].[Parameter]<space>=<space>value

Example:

viscosity.enable = 1

The parameters can be written in any order and none are compulsory as each parameter has a default value.

You can comment a line using the # character.

Example of .msp file for BioSpring

The following example file parameterizes a simulation run with a 2 fs timestep for 1000 steps. The viscosity is set to 0.1 Da.fs-1 and the steric interaction is set to the linear mode with a 8Å cutoff.These parameters are describe in the next section of this manual.

#001_GKinase - Molecular Simulation Parameter file

#fs
simulation.timestep = 2.0
simulation.nbsteps = 1000

#Da.fs-1
viscosity.enable = 1
viscosity.value = 0.1

#kJ.mol-1.A-2
spring.enable = 1
spring.scale = 1

#A
steric.enable = 1
steric.gridscale = 1
steric.cutoff = 8.0
steric.mode = linear

General Simulation Parameters Description

Define the steps and IO settings. The values written here are the default values.

  • simulation.timestep = 1 (fs, float) Timestep in fs used in this run
  • simulation.nbsteps = -1 (integer) Number of simulation steps. The run stops after this step. -1 defines an infinite run and you will have to kill the process manually.
  • simulation.samplerate = 100 (integer) Frequence at which energies are printed on the standard output.
  • pdbtrajectory.enable = 0 (boolean) Enables trajectory writing in pdb format.
  • pdbtrajectory.frequency = 100 (integer) Frequence at which frames are written.
  • pdbtrajectory.path = "" (string) Name of the pdb trajectory file.
  • csvsampling.enable = 0 (boolean) Enables energies logging in csv format.
  • csvsampling.frequency = 100 (integer) Frequence of energy logging.
  • csvsampling.path = "" (string) Name of the csv energies log.
  • xtctrajectory.enable = 0 (boolean) Enables energies logging in xtc format.
  • xtctrajectory.frequency = 100 (integer) Frequence of energy logging.
  • xtctrajectory.path = "" (string) Name of the xtc energies log.

Spring Network Parameters Description

Define how the spring network behavior. More details are given in the examples.

  • spring.enable = 0 (boolean) Enable spring forces.
  • spring.scale = 1.0 (float) Factor applied on the spring forces.
  • spring.cutoff = 1.0 (float) Factor applied on the spring forces.
  • viscosity.enable = 0 (boolean) Enables a damping factor on the particles.
  • viscosity.value = 1.0 (Da.fs-1, float) Damping factor.

Force Field Parameters Description

In addition to springs interaction, you can define steric (short-range) and electrostatic (long-range) interactions. Steric interactions are simulated by a linear repulsive force or a Lennard-Jones potential. Electrostatic interactions are simulated by Coulomb equation.

A pre-computed electrostatic potential grid from APBS[1] can be use in some case, as well as an implicit membrane potential [2]. Details for these features are given in the appropriate examples. (TODO: define which examples)

  • steric.enable = 0 (boolean) Enable steric interaction.
  • steric.mode = linear (string) Type of steric interaction Can be linear, lennard-jones-8-6Lewitt, lennard-jones-8-6Zacharias, lennard-jones-8-6Amber
  • steric.gridscale = 1 (float) Factor applied on steric forces.
  • steric.cutoff = 1 (Angstroms, float) Cutoff distance for steric calculation.
  • coulomb.enable = 0 (boolean) Enables Coulomb interaction.
  • coulomb.scale = 1.0 (float) Factor applied on electrostatic forces.
  • coulomb.cutoff = 16.0 (Angstroms, float) Cutoff distance for Coulomb. calculation
  • coulomb.dielectric = 1.0 (float) Dielectric constant used in Coulomb equation.
  • potentialgrid.enable = 0 (boolean) Enable APBS potential grid.
  • potentialgrid.path = "" (string) Name of the APBS potential grid file in OpenDX format.
  • potentialgrid.scale = 1 (float) Factor applied on electrostatic forces.
  • densitygrid.enable = 0 (boolean) Enable density grid.
  • densitygrid.path = "" (string) Name of the density grid file in OpenDX format.

Implicit Membrane (IMPALA)

Particles with their transfer energies preconfigured via pdb2spn (using the forcefield and reducerules options) can interact with an implicit membrane according to the IMPALA model.

  • impala.enable = 0 (boolean) Enable IMPALA membrane interaction.
  • impala.scale = 1.0 (float) Factor applied on IMPALA forces.
  • insertionvector.enable = 0 (boolean) Enable Insertion Vector.
  • insertionvector.vector = 0 0 (int int) Set the IDs of the two particles defining the insertion vector.

RigidBody

Switch from flexible spring network dynamics mode to rigid body dynamics mode.

  • rigidbody.enable = 0 (boolean) Enable Rigid Body mode.
  • rigidbody.enablesampling = 0 (boolean) Enable Automatic Sampling of insertion into the implicit membrane.
  • rigidbody.enablemontecarlo = 0 (boolean) Enable Monte Carlo Rigid Body to run exploration of random steps in conformational space.
  • rigidbody.montecarlo_translation_norm = 0.1 (float) Magnitude of translation in angstroms (Å) for the Monte Carlo rigid body.
  • rigidbody.montecarlo_rotation_norm = 0.1 (float) Angle of rotation in degrees (°) for the Monte Carlo rigid body.
  • rigidbody.montecarlo_temperature = 298.1 (float) Temperature in Kelvin (K) for the Monte Carlo simulations rigid body.

Hydrophobicity (experimental)

Add a pseudo-hydrophobicity interaction for multimeric assembly into a rigid body in an implicit membrane.

  • hydrophobicity.enable = 0 (boolean) Enable Hydrophobicity interaction.
  • hydrophobicity.scale = 1.0 (float) Factor applied on Hydrophobicity forces.
  • hydrophobicity.cutoff = 15.0 (Angstroms, float) Cutoff distance for Hydrophobicity.

Probe

The probe is a charged entity used to explore and characterize binding sites through electrostatic interactions.

  • probe.enable = 0 (boolean) Enable probe.
  • probe.enableelectrostatic = 0 (boolean) Enable probe electrostatic interaction.
  • probe.enablesteric = 0 (boolean) Enable probe steric interaction.
  • probe.x = 1.0 (float) Initial x position of the probe.
  • probe.y = 1.0 (float) Initial y position of the probe.
  • probe.z = 1.0 (float) Initial z position of the probe.
  • probe.mass = 1.0 (Da, float) Mass of the probe.
  • probe.epsilon = 1.0 (kJ.mol-1, float) Set the probe's interaction energy.
  • probe.radius = 1.0 (Å, float) Sets the probe's radius
  • probe.charge = 0.0 (e, float) Sets the probe's charge

Automatic Constraints Parameters (not available yet)

You can define automatic constraints to push a group of particles toward another without manual interaction.

  • constraint.enable = 0 (boolean) Enables constraint for this run
  • constraint.src = "" (string) The name of the first selection of atom
  • constraint.dest = "" (string) The name of the second selection of atom
  • constraint.scale = 1.0 (Da.A.fs-2, float) Force module used for the constraint

References

[1]: Jurrus E, Engel D, Star K, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018;27(1):112-128. doi:10.1002/pro.3280
[2]: Ducarme P, Rahman M, Brasseur R. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins. 1998;30(4):357-371.