For researchers using GROMACS, setting up pulling simulations often requires creating custom index groups—say, to specify exactly which atoms or chains to pull. But writing index groups by hand in GROMACS can be awkward, especially when you’re dealing with complex biomolecular systems. The trial-and-error of figuring out topology indices or spending time digging through coordinate files can interrupt your workflow.
If you’ve ever thought “there must be an easier way,” then the GROMACS Wizard Extension in SAMSON can help. Its visual tools let you create index groups in a few clicks—no need to manually enter atom numbers.
What are index groups, and why do they matter?
In GROMACS, an index group is essentially a named list of atoms that you want to do something with—apply restraints, pull, calculate RDFs, etc. Modern simulations often require custom groups, especially for advanced methods like umbrella sampling or center-of-mass (COM) pulling.
Creating these groups by hand means deciphering atom indices and using complex command-line tools. SAMSON’s extension replaces that with a visual interface that understands the meaningful structure of your biomolecule.
From structure to index group in seconds
Let’s say you loaded the 2BEG structural model into SAMSON and want to simulate pulling chain A away from chain B. Here’s how easy it is to create index groups for that:
- Load the system and make sure you’re in the Simulate tab of the GROMACS Wizard.
- Click on Edit index groups to open the index group editor.
- Select chain
Ain the Document view of SAMSON. - Click Generate based on current selection in document.
- Give it a name—like
ChainA—and click Add index group to the list. - Repeat the process for chain
B.
You now have two custom index groups that GROMACS will recognize, and you didn’t have to look up a single atom number. The wizard even lets you test these groups by selecting them in your structure to visually confirm your selection.
Takes the guesswork out of pulling simulations
After defining your index groups, you can proceed to set up the COM pulling settings—for example, pulling chain A from chain B in the z-direction using umbrella sampling. The process becomes not only easier, but less error-prone. No more mismatches between intended selections and what GROMACS actually processes.
Whether you’re a molecular modeler new to GROMACS or an experienced user looking to streamline your setup, visual index group creation in SAMSON saves time and reduces mistakes. You get to focus on science, not the syntax of selection strings.
To learn more about COM pulling simulations in SAMSON’s GROMACS Wizard, check out the full documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/com-pulling/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. If you haven’t already, you can download SAMSON at https://www.samson-connect.net.