Solvate and Run MD [MDPrep] [MDRun]ΒΆ

  • Purpose:

    • This Floe performs MD simulations given one or more complete solutes as input, each to be treated in its entirety in a separate simulation.

  • Method Recommendations/Requirements:

    • The solutes need to have reasonable 3D coordinates, all atoms, and correct chemistry (in particular bond orders and formal charges).

    • Each solute can have multiple conformers but each conformer will be run separately.

    • The starting configuration should not have very high gradients, in particular no bad clashes.

    • Protein components need to be prepared to MD standards: protein chains must be capped, all atoms in protein residues (including hydrogens) must be present, and missing protein loops resolved or capped.

    • Crystallographic internal waters should be retained where possible.

  • Limitations

    • The output produced by this floe is not compatible with the Analyze Protein-Ligand MD floe

    • Currently this floe cannot handle covalent bonds between different components such as ligand, protein, and cofactors.

    • Glycosylation on proteins is truncated and the amino acid is capped with H.

  • Expertise Level:

    • Regular/Intermediate/Advanced

  • Compute Resource:

    • Depends on simulation length; Minimal resources for default 2 ns.

  • Keywords:

    • MD, MDPrep

  • Related Floes:

    • Bound Protein-Ligand MD [MDPrep] [MD]

    • Ligand Bound and Unbound Equilibration for NES [MDPrep] [MD]

    • Short Trajectory MD with Analysis [MDPrep] [MD]

Each input solute is solvated to make a flask with periodic boundary conditions and parametrized according to the selected force fields. A minimization stage is performed on the flask followed by a warm up (NVT ensemble) and three equilibration stages (NPT ensemble). In the minimization, warm up and equilibration stages positional harmonic restraints are applied. At the end of the equilibration stages a production run (default 2ns) is performed on the unrestrained flask.

Promoted Parameters

  • HMR (boolean) : On enables Hydrogen Mass Repartitioning. Not currently implemented in Gromacs
    Default: True
  • md_engine (string) : Select the MD available engine
    Default: OpenMM
    Choices: OpenMM, Gromacs
  • cpu_count_md (integer) : The number of CPUs to run this cube with
    Default: 16 Min: 1 Max: 128
  • gpu_count_md (integer) : The number of GPUs to run this cube with
    Default: 1 Max: 16
  • spot_policy_md (string) : Control cube placement on spot market instances
    Default: Allowed
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • prod_ns (decimal) : Length of MD run in nanoseconds
    Default: 2.0
  • prod_trajectory_interval (decimal) : Trajectory saving interval in nanoseconds
    Default: 0.004
  • protein_ff (string) : Force field parameters to be applied to the protein
    Default: Amber14SB
    Choices: Amber14SB, Amber99SB, Amber99SBildn, AmberFB15
  • ligand_ff (string) : Force field to be applied to the ligand
    Default: OpenFF_2.0.0
    Choices: Gaff_1.81, Gaff_2.11, OpenFF_1.1.1, OpenFF_1.2.1, OpenFF_1.3.1, OpenFF_2.0.0, Smirnoff99Frosst
  • solute (data_source) : Solute input file
  • density (decimal) : Solution density in g/ml
    Default: 1.03
  • salt_concentration (decimal) : Salt concentration (Na+, Cl-) in millimolar
    Default: 50.0
  • out (dataset_out) : MD Dataset out
  • fail (dataset_out) : MD Dataset Failures out

Extra Required Parameters

  • Log Field (Field Type: String) : The field to store messages to floe report
    Default: Log Field
  • Log Field (Field Type: String) : The field to store messages to floe report
    Default: Log Field