Plain Molecular Dynamics [MDRun]ΒΆ
Purpose
This floes runs unrestricted plain Molecular Dynamics simulations on input datasets with fully set up, parameterized, and ready-to-run flasks. It makes possible long MD simulations in Orion, running MD simulations in chunks by using a floe cycle topology.
Method Recommendations/Requirements:
If for some reason the floe along the cycling should stop, the user can try to restart the floe by using the recovery output
One input is required:
An Orion Dataset having records with a completely set up and ready-to-run MD flask, including solvent and counterions, and with the force field parameter applied. This can be produced by running one of the MD floes like the Short Trajectory MD or the Bound Protein Ligand MD floes, but it is not a prior restricted to protein-ligand flasks.
Expertise Level:
Regular
Compute Resource:
High
Keywords:
MD, Analysis
Related Floes:
Ligand Bound and Unbound Equilibration for NES [MDPrep] [MD]
Bound Protein-Ligand MD [MDPrep] [MDRun]
Analyze Protein-Ligand MD [MDAnalysis]
When the floe completes, the produced chunked trajectories are uploaded to s3 as files and can be downloaded for analysis. In Addition the output dataset will have on its records the references to the produced trajectories which can then be extracted by using the MDDataRecord API.
If the starting dataset was generated by using the Bound Protein-Ligand floe or the Ligand Bound and Unbound Equilibration floe than the cycle floe output can be analyzed by the Analyze Protein-Ligand MD floe, although very large trajectories can cause problems for the clustering step in the analysis.
Promoted Parameters
md_engine (string) : Select the MD EngineDefault: OpenMMChoices: OpenMM, Gromacs HMR (boolean) : Give hydrogens more mass to speed up the MDDefault: True out (dataset_out) : MD Dataset out recovery (dataset_out) : Recovery Dataset out flask (data_source) : Ready-to-run Flask input dataset fail (dataset_out) : Output dataset to write to time (decimal) : Total simulation time in nanosecondsDefault: 10 trajectory_interval (decimal) : Trajectory saving interval in nanosecondsDefault: 0.01 reporter_interval (decimal) : Reporter saving interval in nanosecondsDefault: 0.01 cube_max_run_time (decimal) : Max Cube Running Time in hrsDefault: 10