When setting up a molecular dynamics simulation involving pulling or restraining specific molecular parts, having precise control over which atoms belong to which group is crucial. This is especially important in center-of-mass (COM) pulling simulations where specifying exactly which atoms are being pulled — and from what reference — makes all the difference.
In GROMACS, this is done through index groups. By default, GROMACS generates standard groups like Protein, Water, Ions, etc. But what happens if you want to isolate a particular chain as a group? Or a selection of residues? This is where custom index groups come into play — and the GROMACS Wizard in SAMSON makes this manageable through its visual interface.
Why You Might Need Custom Index Groups
Let’s say you’re simulating the pulling of chain A away from chain B in a molecular complex, such as 2BEG, a protein that contains 5 chains. The default index groups won’t help — you specifically need to define the atoms of chain A and chain B as separate groups. This becomes your pulling and reference points, respectively.
Creating these custom groups in traditional GROMACS involves command-line usage and editing with make_ndx. With SAMSON’s GROMACS Wizard, however, the process is visual and streamlined.
Step-by-Step: Defining Index Groups in SAMSON
After loading your molecular system (e.g., 2BEG) into SAMSON, here’s how to define specific chains as index groups:
- Open the Index Groups window from the GROMACS Wizard’s Simulate tab by clicking Edit index groups.
- Select the target chain (e.g., chain A) in the Document view.
- In the Index Groups window, click Generate based on current selection in document; this creates a selection string automatically.
- Set a name (e.g.,
ChainA) and click Add index group to the list.
Repeat the process for chain B or any other group you need.
Verifying and Using Your Groups
After the groups are added, you can test them by selecting one from the list and clicking Select in document based on selection string. This will highlight the corresponding atoms in your workspace, helping you confirm your selections visually.
What Next?
Once defined, these groups become available throughout the GROMACS Wizard workflow — particularly when setting up COM pulling coordinates, restraints, or any simulation step where precision grouping is needed. Combined with the ability to simulate locally or in the cloud, this makes SAMSON a practical environment for researchers juggling complex biomolecular systems.
Learn more in the full tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.