Pulling one molecular group away from another sounds straightforward: define the groups, choose a direction, and run the simulation. In practice, a common source of trouble is the periodic box. If the box is too short along the pulling direction, the pulled group can interact with its periodic image, making the intended separation difficult to interpret.
This workflow uses the 2BEG system as an example: chain A is pulled away from chain B along the z-axis, while chain B is restrained. The central planning rule is simple: choose the box dimensions with the full pulling displacement and periodic boundary conditions in mind.
Plan the box around the displacement
For the example, the target pull distance is 5 nm in the z-direction. The minimum-image convention means that the pull distance must remain less than half the box length along the pulling direction. A 10 nm z-dimension would therefore only meet the basic twice-the-pull-distance calculation. The tutorial adds extra room on both sides, setting the z-length to 12 nm to better accommodate parts of the pulled chain extending beyond the target displacement.
In GROMACS Wizard, the example uses an orthorhombic box. First compute the fitted box, then set the box lengths to 6.5 nm x 4.5 nm x 12 nm. The center is adjusted to 0.5 x 0.5 x 0.2 of the box size rather than centering the system automatically. The placement helps allocate space in the pulling direction. If your pull direction is not aligned with a box axis, orient the system before setting up the box.
Define the groups you actually mean to pull
Pulling parameters operate on index groups. If the desired chains are not among the default groups, create custom ones and verify their selections before running. For this example, the groups are named ChainA and ChainB. Select each chain in SAMSON’s Document view, generate an index group from the current selection, and add it to the list. Testing a group by selecting its atoms in the document is a useful way to catch an incorrect selection before it becomes part of a simulation.
Keep the reference group in place
For the production simulation, apply position restraints to chain B so it remains the reference while chain A moves away. Then add a COM pulling coordinate with the following settings: umbrella type, distance geometry, group 1 as chain A, group 2 as chain B, and start = yes. Set the direction to N N Y to pull along z, with an initial distance of 0 nm.
The example uses a rate of 0.01 nm/ps. Over a 0.5 ns simulation, that corresponds to 500 ps × 0.01 nm/ps = 5 nm. The force constant is 1000 kJ mol^-1 nm^-2. Checking the units and multiplication before starting makes it easier to confirm that the planned displacement matches the simulation duration.
Check what the simulation reports
After the run, inspect the trajectory to see the structural motion, and review the pull-coordinate and pull-force plots. Together, they show how the separation changes over time and how the force responds during the pull. These outputs are useful checks on whether the simulation followed the intended coordinate; they are also the starting point for the tutorial’s subsequent umbrella-sampling workflow.
The broader preparation sequence matters too: prepare and neutralize the system, minimize it, equilibrate it, and then run production MD with the pulling settings. For the 2BEG example, preparation uses AMBER03, TIP3P water, neutralizing ions, and additional 100 mM NaCl. The full walkthrough provides the corresponding settings and interface screenshots.
For the complete workflow, see the GROMACS Wizard COM Pulling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.