Extend MD Simulations

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

  • Tutorials and Further Reading:

  • Purpose

    • This Floe extends existing MD simulations. It takes input datasets with fully set up, parameterized, and ready-to-run flasks and runs additional MD stages. If a simulation is unexpectedly interrupted before all cycles are complete, it can also be restarted using the recovery output.

    • Method Recommendations/Requirements:

      • If the Floe stops before completing all cycles, the user can restart it 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 parameters applied. The dataset may contain completed MD stages to extend, or unfinished cycles to restart from the recovery output. 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 priori restricted to protein-ligand flasks.

  • Expertise Level:

    • Regular

  • Compute Resource:

    • High

  • Keywords:

    • MD

  • Related Floes:

    • Bound Protein-Ligand MD

    • Short Trajectory MD with Analysis

    • Analyze Protein-Ligand MD

    • Solvate and Run MD

    • FE-NES for Binding Affinity Prediction

When the Floe completes, it produces a Trajectory Downloader Floe report. The report can be used to download all trajectories associated with the dataset, including previously completed and newly extended trajectories.

If the starting dataset was generated by using the Bound Protein-Ligand Floe or the Short Trajectory MD with Analysis Floe, then the Floe MD 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

Title in user interface (promoted name)

Outputs

MD Output Dataset (md_out): Output dataset of extended MD simulations.

  • Required

  • Type: dataset_out

  • Default: md_output

MD Recovery Output Dataset (md_recovery_out): This is an optional MD recovery dataset generated when the ‘Save MD recovery records’ parameter of the ‘MD Recovery Switch’ cube is On.

  • Required

  • Type: dataset_out

  • Default: md_recovery

Trajectory Downloader (traj_downloader): Title for the trajectory downloader Floe Report.

  • Type: string

  • Default: Trajectory Downloader

Failed Output Dataset (fail_out): Output dataset of failed calculations.

  • Required

  • Type: dataset_out

  • Default: Failed Output for Extend MD Simulations

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: decimal

  • 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

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]

Time (time): Total simulation time in nanoseconds.

  • Type: decimal

  • Default: 10

Trajectory Interval (trajectory_interval): Trajectory saving interval in nanoseconds.

  • Type: decimal

  • Default: 0.01

Reporter Interval (reporter_interval): Reporter saving interval in nanoseconds.

  • Type: decimal

  • Default: 0.01

Cube Max Run Time (cube_max_run_time): Max cube running time in hours.

  • Type: decimal

  • Default: 1