Solvate and Run MD [MDPrep] [MDRun]¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Product-based/Molecular Dynamics/GROMACS
Product-based/Molecular Dynamics/OpenMM
Role-based/Computational Chemist
Role-based/Medicinal Chemist
Task-based/Molecular Dynamics
Solution-based/Hit to Lead/Target Preparation/Generic MD simulation
Description
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
Title in user interface (promoted name)
Solvation Parameters
density (density): Solution density in g/ml
Type: decimal
Default: 1.03
Salt Concentration (salt_concentration): Salt concentration (Na+, Cl-) in millimolar
Type: decimal
Default: 50.0
Restrain protein tumbling (restraint_protein_tumbling): Restraining protein tumbling allows for a smaller flask
Type: boolean
Default: False
Choices: [True, False]
Restrain protein tumbling wt (restraint_protein_tumbling_Wt): Restraint weight for pre-defined xyz atom restraints in kcal/(mol A^2)
Type: decimal
Default: 0.1
CPU GPU Spot Policy Selection
CPUs (cpu_count_md): The number of CPUs to run this cube with
Type: integer
Default: 12
GPUs (gpu_count_md): The number of GPUs to run this cube with
Type: integer
Default: 1
Spot policy (spot_policy_md): Control cube placement on spot market instances
Type: string
Default: Allowed
Choices: [‘Allowed’, ‘Preferred’, ‘NotPreferred’, ‘Prohibited’, ‘Required’]
MD Setup Parameters
Ligand Force Field (ligand_ff): Force field to be applied to the ligand. The OpenFF >=1.3.1 and Custom force fields may be augmented with bespoke force field parameters by turning on ‘Use Bespoke Parameters When Available’ and providing SMIRNOFF format parameters on the input record.
Required
Type: string
Default: OpenFF_2.2.0
Choices: [‘Gaff_1.81’, ‘Gaff_2.11’, ‘OpenFF_1.1.1’, ‘OpenFF_1.2.1’, ‘OpenFF_1.3.1’, ‘OpenFF_2.0.0’, ‘OpenFF_2.2.0’, ‘Smirnoff99Frosst’, ‘Custom’]
Custom Ligand Force Field File (custom_offxml_file_in): One or more SMIRNOFF XML files defining the force field to be applied to the ligand. This input is required when ‘Ligand Force Field’ is set to ‘Custom’.
Type: file_in
Protein Force Field (protein_ff): Force field to be applied to the protein.
Required
Type: string
Default: Amber14SB
Choices: [‘Amber14SB’, ‘Amber99SB’, ‘Amber99SBildn’, ‘AmberFB15’]
Cube max run time (cube_max_run_time): Max Cube Running Time in hrs
Type: decimal
Default: 1
MD Engine (md_engine): Select the available MD engine
Type: string
Default: OpenMM
Choices: [‘OpenMM’, ‘Gromacs’]
Hydrogen Mass Repartitioning (HMR): Give hydrogens more mass and increase the MD integration time step from 2 to 4 fs
Type: boolean
Default: True
Choices: [True, False]
NPT Production Runtime (prod_ns): NPT simulation production time in nanoseconds
Type: decimal
Default: 2.0
Trajectory Interval (prod_trajectory_interval): Trajectory saving interval in nanoseconds
Type: decimal
Default: 0.004