In a steered molecular dynamics setup, choosing the pulling coordinate is only part of the problem. The simulation box matters too: with periodic boundary conditions, a molecule can encounter its periodic image before it has travelled the distance you intended. That can make the setup difficult to interpret.
This example uses GROMACS Wizard in SAMSON to pull chain A of the 2BEG system away from chain B. The key planning rule is simple: the pull distance must be less than half the box length along the pulling direction, taking periodicity into account. The example turns that rule into a concrete box size and a set of pulling parameters.
Plan the box around the motion
Suppose the target is to pull chain A by 5 nm from chain B along the z-axis. A z-length of exactly 10 nm would put the pull distance at half the box length, leaving little room for the system’s position and movement. The tutorial instead uses a 12 nm z dimension: twice the 5 nm pull distance, plus 1 nm of additional space at each end.
For the example, the full orthorhombic box is set to 6.5 nm × 4.5 nm × 12 nm. After computing the fitted box, set the box lengths explicitly and turn off Center in box. The system’s center is set to 0.5 × 0.5 × 0.2 of the box dimensions. Positioning the system this way helps reserve room in the direction of travel; the box should be considered together with the pull distance, not as an afterthought.
If the desired pulling direction is not aligned with a box axis, orient the structure first. SAMSON’s move tools or the structure context menu’s Move selection > Align… command can be used to align it with a suitable axis or plane.
Make the two groups explicit
COM pulling acts on groups, so define the pulled and reference groups deliberately. In this example, create custom index groups named ChainA and ChainB from selections in the document. In GROMACS Wizard, use Edit index groups, select each chain in the Document view, generate a selection string from the current selection, and add the group to the list. If the system is not loaded in SAMSON, load it first so the groups can be generated from document selections.
Check that each custom group selects the intended chain before running. A quick selection check can catch a group-definition mistake while it is still easy to fix.
Keep the reference chain in place
The example restrains chain B during production, while chain A is pulled. This gives the pull coordinate a clear reference group. In the production parameters, activate the position restraint for chain B; the tutorial also activates position restraints for chains during NPT equilibration. Energy minimization is run with the chain and water position-restraint options left unchecked.
For the production run, the example uses a 0.5 ns simulation with a 2 fs time step. Its COM pulling settings are: type umbrella, geometry distance, group 1 chain A, group 2 chain B, and start = yes. Set the distance components to N N Y for z-direction pulling, with an initial value of 0 nm, a rate of 0.01 nm/ps, and a force constant of 1000 kJ mol-1 nm-2. The rate corresponds to 5 nm over 500 ps.
Check the outcome, not just the settings
After the simulation, inspect the trajectory and the generated pull-coordinate and pull-force plots. The coordinate plot helps you see how the displacement develops over time; the force plot shows how the force changes during the pull. These outputs are useful checks on what the simulation actually did, and the resulting trajectory can be used as a starting point for umbrella sampling.
The broader lesson is to plan the periodic box, define both groups, and set the restraint and pulling direction as one connected setup. For the complete workflow and screenshots, see the GROMACS Wizard COM Pulling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.