Pulling one molecular group away from another sounds straightforward: choose two groups, set a direction and distance, and run molecular dynamics. In practice, a common source of trouble is easier to overlook: the simulation box is periodic. If the box is too short along the pulling direction, the moving molecule can interact with a periodic image of the system before it reaches the intended separation.
This example shows how to plan a center-of-mass (COM) pulling setup in GROMACS Wizard, using the 2BEG system. Chain A is pulled away from chain B along the z-axis. The central lesson is to plan the box and the pull coordinate together—not as separate settings.
Start with the geometry
For the example, the target displacement is 5 nm in the z-direction. Under the minimum image convention, the pull distance must be less than half the box length along the pulling direction. A 5 nm pull therefore calls for a z dimension greater than 10 nm. The tutorial uses a 12 nm z dimension, leaving additional room in case parts of the pulled chain extend beyond the nominal displacement.
The other box dimensions are set to 6.5 nm and 4.5 nm, giving a box of 6.5 nm × 4.5 nm × 12 nm. The system’s center is positioned at 0.5 × 0.5 × 0.2 of the box dimensions rather than automatically centered. This places the structure with the pulling direction in mind.
If the molecule’s intended pulling axis is not aligned with a box axis, orient the system before preparation. SAMSON provides move editors and the structure’s Move selection > Align… command for aligning it to a suitable axis or plane.
Prepare groups that mean what you think they mean
GROMACS uses index groups to define the atoms involved in a pull coordinate. If the groups you need are not among the defaults, create custom groups from the molecular selections. In this example, add groups named ChainA and ChainB by selecting each chain in the Document view and generating an index group from the current selection.
It is worth checking each group before running: select it in the index-group list and use Select in document based on selection string. This simple verification helps catch a group-definition mistake before it becomes a confusing trajectory or an unexpected pulling coordinate.
Keep the reference group in place
During production MD, the example applies a position restraint to chain B so it stays in place while chain A is pulled away. This is distinct from the COM pulling coordinate itself: the restraint helps keep the reference chain from drifting, while the pull definition specifies the relative motion to simulate. During NPT equilibration, the tutorial activates position restraints for the chains; for production, it specifically restrains chain B.
Translate the target into pull settings
The example uses an umbrella-type pull coordinate with distance geometry, chain A as group 1, and chain B as group 2. The pull starts at 0 nm and uses the z component (N N Y). Its rate is 0.01 nm/ps, which gives the intended 5 nm displacement over a 0.5 ns production run:
0.01 nm/ps × 500 ps = 5 nm
The force constant is 1000 kJ mol-1 nm-2. Thinking through the units is a useful check: a rate that looks small per picosecond can produce a substantial displacement over hundreds of picoseconds.
Check the output, not just the settings
After the simulation, load the resulting trajectory to inspect the motion. The generated pull-coordinate and pull-force plots help show how displacement and force change over time. In the example, the force builds until it is sufficient to overcome the internal restoring forces between the chains. If the motion or plots do not match the intended setup, revisit the group definitions, pulling direction, rate, and box length before interpreting the result.
This pulling workflow can provide starting output for umbrella sampling, where configurations along the pulling coordinate are used to create windows for free-energy analysis.
For the complete workflow and interface details, see the GROMACS Wizard COM Pulling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.