Pulling one molecular group away from another sounds straightforward: choose the groups, set a direction, and run a 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 a periodic image of the system before it reaches the intended distance. The result is a setup that may not represent the separation you meant to simulate.
This walkthrough focuses on the part of center-of-mass (COM) pulling that is easy to underestimate: coordinating the pull distance, box dimensions, and reference group. It uses the 2BEG system and GROMACS Wizard in SAMSON. The example pulls chain A away from chain B along z, while restraining chain B.
Start with the distance and the periodic box
Before choosing box dimensions, decide how far you intend to pull and in which direction. In this example, chain A is pulled 5 nm from chain B along the z-axis. Under the minimum image convention, the pull distance must remain less than half the box length in the pulling direction. A 5 nm pull therefore calls for a z dimension greater than 10 nm, with additional room desirable in case parts of the pulled chain extend farther.
The tutorial uses an orthorhombic box measuring 6.5 nm x 4.5 nm x 12 nm. The extra space in z gives a margin beyond twice the nominal pull distance. The system’s center is also positioned deliberately: the “Center in box” option is turned off, and the center is set to 0.5 x 0.5 x 0.2 of the box dimensions. That places the system toward one end of the long axis, leaving space in the pulling direction.
If your pulling direction is not aligned with a box axis, orient the structure before preparing the system. The tutorial suggests using SAMSON’s move tools or the structure’s context menu to align it with a suitable axis or plane. The key is to make the chosen box dimension correspond to the actual direction of travel.
Make the two groups explicit
COM pulling depends on selecting the intended groups, so do not assume the default GROMACS index groups will contain the chains you need. In this example, create custom index groups named ChainA and ChainB. Load the system in SAMSON, select each chain in the Document view, and use the Index Groups window’s “Generate based on current selection in document” command. Add each generated group to the list, then verify a group by selecting it and using “Select in document based on selection string.”
Keep the reference group in place
For this example, chain B is the reference and chain A is pulled away from it. During production MD, activate the position restraint for chain B so it stays in place while chain A moves. This restraint is distinct from the COM pulling definition: the restraint helps keep the reference chain in place, while the pull parameters specify the groups and coordinate used for the pulling motion.
In the COM pulling section, add a pulling group and set: type umbrella, geometry distance, group 1 to chain A, group 2 to chain B, and start to yes. For a z-direction pull, use N N Y for the distance components. Set the initial distance to 0 nm, the rate to 0.01 nm/ps, and the force constant to 1000 kJ mol^-1 nm^-2.
The rate is consistent with the intended schedule: 0.01 nm/ps over 500 ps moves the pull coordinate by 5 nm. The example production run is 0.5 ns with a 2 fs timestep. Thinking through the units before launching is a useful way to catch mismatches between the rate and the planned run duration.
Use the output to check what happened
After the preparation, minimization, NPT equilibration, and production steps, inspect the generated trajectory to visualize the pulling. The production run also generates plots for pull force and coordinates. The coordinate plot helps you see displacement along the pull coordinate over time; the force plot shows how the force changes as the chains are separated. These outputs provide a practical check that the configured pull produced the motion you intended.
The pulling results can be used as a starting point for umbrella sampling, where configurations from the pulling workflow are used to generate umbrella windows. For the full workflow and the interface details, see the GROMACS Wizard COM Pulling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.