Plain Gromacs [MDRun]

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/Molecular Dynamics/GROMACS

  • 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 using GROMACS given ready-to-go input .tpr files.

  • Method Recommendations/Requirements:

    • The input .tpr files need to be correctly prepared (no checking is done).

  • Limitations

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

  • Expertise Level:

    • Advanced: this Floe is for GROMACS MD experts.

  • Compute Resource:

    • Depends on simulation length as given in the .tpr input file.

  • Keywords:

    • MD

  • Related Floes:

    • Solvate and Run MD [MDPrep] [MD]

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

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

The Floe will run the MD in stages, where each stage runs for n hours (10hrs default) in between checkpointing in a recovery dataset. The trajectory accumulated in each stage is stored in gromacs file format in the user’s filespace. The Gromacs Cube then restarts from the recovery dataset and runs for an additional n hours in a cycle until completing the number of md steps specified in the input .tpr file. If the recovery dataset is provided as input, Gromacs will start from the last checkpoint saved in the recovery dataset. If both .tpr and recovery dataset files are provided the recovery dataset will supersede the .tpr file.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input Dataset (in): The Dataset used for restarting. OPTIONAL

  • Type: data_source

Gromacs Parameters

Gromacs Tpr (tpr): A GROMACS 2023 portable binary run input (.tpr) file

  • Type: file_in

Prefix Name (Flask prefix): The system prefix name

  • Required

  • Type: string

  • Default: Flask

verbose (verbose): Enable/Disable Gromacs Std Output

  • Type: boolean

  • Default: False

  • Choices: [True, False]