Creating Custom Index Groups for COM Pulling in GROMACS Wizard

One of the common challenges in setting up center-of-mass (COM) pulling simulations using GROMACS is defining the correct groups of atoms when default index groups are not sufficient. If you’re dealing with multi-chain molecular systems and want to precisely control pulling forces – for instance, pulling one protein chain from another – you’ll probably need to create custom index groups. Fortunately, the GROMACS Wizard in SAMSON makes this task more visual and intuitive than manually editing index files.

Let’s take a practical look at this through a case involving the 2BEG protein system (which contains five chains). In this example, we want to pull chain A away from chain B during a production MD step. To do that, we need to create two specific index groups: one for chain A and one for chain B.

Why Custom Index Groups Matter

When GROMACS generates its default index groups, it includes general categories like Protein, Water, and Ions. But in many molecular modeling scenarios, especially when simulating interactions between specific chains or domains, these broad categories aren’t specific enough. Custom index groups allow you to:

  • Apply pulling, restraints, or forces to precise subsets of atoms
  • Track motions of individual domains or chains
  • Tailor the simulation parameters with more granularity

Creating Custom Groups in SAMSON

To create custom index groups in the GROMACS Wizard Extension, do the following:

  1. First, ensure the structure (e.g., 2BEG) is loaded in SAMSON using the Load button in the “Input” section of the Simulate tab.
  2. Click on the Edit index groups button. A window showing existing index groups will appear.
  3. Select chain A in the Document view.
  4. In the Index Groups window, click on Generate based on current selection in document. This produces a selection string for the currently highlighted atoms.
  5. Name the group “ChainA” and click Add index group to the list.

Add an index group for chain A

Repeat the process for chain B. In a few clicks, you’ve created custom groups without having to manually edit index.ndx files or rely on command-line tools.

To check your selection, simply highlight a group and click Select in document based on selection string. This selects the atoms affiliated with the index group, making it immediately clear whether the group was defined correctly.

Select nodes from an index group

How This Fits into COM Pulling Workflows

Once your custom groups are created, they can be directly used in the Production MD step to set up COM pulling. Whether you’re performing umbrella sampling or simulating force-induced conformational changes, having these groups defined saves time and avoids mistakes.

By managing everything visually – from selection to naming to verification – SAMSON reduces the risk of selecting the wrong atoms and removes the need to learn selection syntax or use external editors.

Wrap-Up

Defining index groups doesn’t have to be error-prone or tedious. With SAMSON’s graphical interface and the GROMACS Wizard Extension, you can generate and validate custom index groups in just a few steps – even for complex systems with multiple chains.

To get a detailed walkthrough of the full COM pulling workflow, including system preparation, NPT equilibration, and MD simulation, visit the official 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 get SAMSON at https://www.samson-connect.net.

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