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GROMACS Wizard - Batch computations#

This section is a part of the GROMACS Wizard tutorial.

This tutorial demonstrates how to perform batch computations using GROMACS Wizard for:

The batch project allows you to easily launch the next steps (minimization, equilibration, simulation) for the whole batch (locally or in the cloud) with the same parameters.

A single system with many conformations#

To use an existing trajectory, load it in SAMSON via Home > File > Open (Ctrl/Cmd + O) or simply drag-and-drop a trajectory in SAMSON.

Creating a trajectory or conformations in SAMSON

You can also create a trajectory or a set of conformation in SAMSON using various tools:

Getting conformations for specific frames of a trajectory

If as initial conformations you want to use only some of the trajectory frames, then you can export conformations for specific frames using one of the two ways:

  • Go through the trajectory frames using the Inspector and create conformations via Edit > Conformation for your frames of choice.
  • Create conformations for all the frames in the trajectory - select the path in the Document view, right-click on it, and in the context menu click on Path > Create conformations from path - and then delete the unwanted conformations.

Set up the preparation#

Once you have a trajectory or a set of conformations you want to use as initial frames you are ready to go:

  1. Open the Prepare tab in the GROMACS Wizard.
  2. Set molecular system: Select a structural model from the Document view and set it as the system. Please refer to Step 1: Prepare - Set the molecular system.
  3. Check the [Optional] Batch preparation box.

  4. Select initial conformations: Select in the Document view a set of conformations or a single trajectory (a path node) corresponding to the chosen system. To specify the initial conformations/states for subprojects in the batch project you have two options:

    • select a set of conformations - each conformation will act as an initial state for a subproject.
    • select a path - each frame will act as an initial state for a subproject.

  5. Click the Set conformations or a path button. You should see the number of conformations next to it and you can use the slider to go through the conformations.

  6. Follow the tutorial Step 1: Prepare:

    1. Choose the force field and solvent. Please refer to Step 1: Prepare - Choose the model.
    2. Optional: You can add custom index groups that might later be useful for analysis or during the simulation (e.g., as pull coordinate groups). Please refer to Step 1: Prepare - Adding custom index groups.
    3. Specify ions. Please refer to Step 1: Prepare - Add ions.

  7. Specify the periodic box: whether it should be based on all the conformations (option: Box lengths) or per conformation (option: Solute-box distance). Please refer to the Define the periodic box section below.

  8. Click Prepare.

Note

The prepared batch project will contain numbered subfolders each representing a fully separate project. You can run the next steps on the whole batch project or separate subfolders.

Define the periodic box#

Please refer to Step 1: Prepare - Define the periodic box.

For the batch project, the periodic box is set in one of the two ways:

  • Based on all the conformations via the Box lengths option. You can specify the box size. On fitting it will fit the box tightly to your system – you will need to increase the size as needed to ensure the minimum image convention. This option also allows you to move the box to position the system in it. For the batch project, the initial box size is determined based on all the conformations or the whole path – choose this option if you want the box size to be the same for the whole batch.
  • Per conformation via the Solute-box distance option. You can specify the distance between the system (solute) and the box. At least 1 nm is recommended to ensure the minimum image convention. For the batch project, the box sizes will be different for each conformation or frame of the path.

If you do not necessarily need to have the same box sizes for all the conformations then you can choose the Solute-box distance option (set the distance to be at least 1 nm) allowing you to have smaller boxes for more compact conformations leading to a decrease in the computational time.

Tip

Once you set the periodic box you can use the slider in the Batch preparation box to see how the periodic box fits the conformations.

A set of different systems#

You can prepare a batch computation (minimization, equilibration, and simulation) for different systems (e.g., multiple systems with different proteins):

  1. Prepare each system separately - please refer to the Step 1: Preparation.
  2. Put all the resulting folders with prepared systems (they have the suffix "-prepare") in the same "batch" folder. You can rename the subfolders, if you wish (e.g., by PDB identifiers), or just leave them as is - the subfolder names will be preserved at the next steps.
  3. In the minimization step and other steps later, choose the input as "From batch folder" and select the "batch" folder (see the section below).

Note

When running batch computations on different systems, you should not use in MD parameters index groups or position restraint (POSRES) records specific to a particular system and not present in other systems in the same batch. Usually, this is used in some advanced options for complex systems and, for example, is not often used for just protein systems.

Minimize, equilibrate, and simulate in batch#

Once the batch project has been prepared, you can follow the same steps as for a single project:

Choose From batch folder as the input path (note: if you click the auto-fill button (Auto-fill button) it will be set automatically based on the previous run).

Choose input type

You can launch the computations locally or in the Cloud (see Launching computations in the Cloud).

When launching local computations for a batch project they will be added as local jobs - a separate job per a subfolder in the batch project - you can access them in the Local jobs window and see their status, change their priority (order), cancel or stop them, import them or open their folders.

Open local jobs

When launching Cloud computations for a batch project, a separate Cloud job per a subfolder in the batch project will be created - you can access them in the Cloud jobs window and see their status, cancel or stop them, download and import them.