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 GromacsDefault: True md_engine (string) : Select the MD available engineDefault: OpenMMChoices: OpenMM, Gromacs cpu_count_md (integer) : The number of CPUs to run this cube withDefault: 16 Min: 1 Max: 128 gpu_count_md (integer) : The number of GPUs to run this cube withDefault: 1 Max: 16 spot_policy_md (string) : Control cube placement on spot market instancesDefault: AllowedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required prod_ns (decimal) : Length of MD run in nanosecondsDefault: 2.0 prod_trajectory_interval (decimal) : Trajectory saving interval in nanosecondsDefault: 0.004 protein_ff (string) : Force field parameters to be applied to the proteinDefault: Amber14SBChoices: Amber14SB, Amber99SB, Amber99SBildn, AmberFB15 ligand_ff (string) : Force field to be applied to the ligandDefault: OpenFF_2.0.0Choices: 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/mlDefault: 1.03 salt_concentration (decimal) : Salt concentration (Na+, Cl-) in millimolarDefault: 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 reportDefault: Log Field Log Field (Field Type: String) : The field to store messages to floe reportDefault: Log Field