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 a set of initial conformations of a single molecular system.

To use an existing trajectory, load it in SAMSON. You can also create a trajectory or a set of conformation in SAMSON using various tools:

If you do not want to use all of the trajectory frames as initial conformations then you can create conformations for specific frames as follows:

  • Go through the trajectory frames using the Inspector and create conformations via Edit menu > 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.

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

Open the Prepare tab in the GROMACS Wizard and follow the tutorial Step 1: Prepare by choosing the batch preparation and setting the conformations or a path. Please see below the brief description of the steps from the mentioned tutorial.

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.

Choose the model

Choose the force field and solvent. Please refer to Step 1: Prepare – Choose the model.

Set system

Choose the structural model from the document and set it as the system. Please refer to Step 1: Prepare – Set the molecular system.

Add index groups

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.

Set initial conformations

Activate the batch project by toggling “[Optional] Batch project” box.

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.

Once you selected a set of conformation or a path from the document, click “Set conformations or a path“. You should see the number of conformations next to it and you can use the slider to go through the conformations.

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 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 conformationSolute-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.

Note: 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.

Add ions

Choose ions as described in Step 1: Prepare – Add ions.

Minimize, equilibrate, and simulate

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

Please choose the batch project as the input path (if you click the auto-fill button it will be set automatically based on the previous run).

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

Note that 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.

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