Easily Selecting Chains for Pulling in GROMACS Simulations with SAMSON

When setting up molecular dynamics simulations in GROMACS, many researchers face a recurring hurdle: defining custom index groups to isolate specific molecular components—like protein chains—for analysis or for applying pulling forces. This can be tedious and error-prone when done manually using GROMACS command-line tools, especially for newcomers.

If you’re preparing a center-of-mass (COM) pulling simulation—where, for example, you pull chain A away from chain B—SAMSON’s GROMACS Wizard makes this part easy and interactive. Here’s how.

Selecting Chains in the SAMSON Interface

Instead of typing atom numbers or editing index files by hand, SAMSON lets you define index groups graphically. This process is intuitive and saves time:

  1. Load your system into SAMSON. For example, use the 2BEG structure by fetching it from the PDB database.
  2. In the Document view, select chain A—the one you intend to pull.
  3. Click the Edit index groups button in the Simulate tab of the GROMACS Wizard.
  4. Click Generate based on current selection in document. This auto-generates a selection string for your custom group.
  5. Name it ChainA and click Add index group.

Add an index group for chain A

Repeat the process for chain B, which will remain fixed (i.e., restrained during MD).

Add an index group for chain B

Verifying Your Groups

You can check your new index groups by selecting one and clicking Select in document based on selection string.

Select nodes from an index group

Why This Matters

Having clearly defined index groups from the start ensures that pulling forces, restraints, and analyses act on the right parts of your system. It also streamlines integration with other steps, like directive generation for pulling simulations. Besides, handling this in a graphical environment means fewer mistakes and an easier learning curve for students or early-career scientists.

The GROMACS Wizard even shows the full list of default GROMACS groups (like Protein, Water, Ions) and supports this kind of custom definition through its seamless interface. No editing .ndx files manually. No rerunning commands because of missed atom selections. It gets you to simulation—faster and more confidently.

To see the full COM pulling tutorial, including how to run the simulation and plot the results, visit the original documentation page: https://documentation.samson-connect.net/tutorials/gromacs-wizard/com-pulling/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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