Pulling one molecular group away from another can be a useful step toward umbrella sampling—but a setup that looks reasonable in the interface can still be compromised by a too-small periodic box or incorrectly defined groups. The key is to plan the geometry and confirm what is being pulled and what is being held in place before launching the simulation.
This walkthrough focuses on those practical decisions in a center-of-mass (COM) pulling workflow using GROMACS Wizard in SAMSON. The example uses the 2BEG system: chain A is pulled away from chain B along the z-axis, while chain B is restrained during production.
1. Plan the box around the pull distance
Periodic boundary conditions mean the simulation box repeats in space. As a result, a pulled molecule can encounter an image of the system across a box boundary if there is not enough room in the pulling direction. The minimum image convention puts a useful constraint on the setup: the pull distance should be less than half the box length along that direction.
In this example, the target displacement is 5 nm along z. The z dimension therefore needs to be at least 10 nm, with extra room to accommodate parts of the pulled chain. The tutorial uses a 12 nm z dimension, and box lengths of 6.5 × 4.5 × 12 nm. It also places the system’s center of mass at 0.5 × 0.5 × 0.2 of the box, rather than centering it, to allow space in the direction of travel.
If the intended pulling axis is not aligned with a box axis, orient the system before defining the box and pulling direction. SAMSON provides move and alignment tools for this. The important check is that the box has enough length along the actual pull direction—not just that the molecule fits inside it at the start.
2. Define the two groups explicitly
COM pulling acts on index groups. If the groups you need are not among the default GROMACS groups, add custom groups before setting the pull coordinate. For the 2BEG example, create groups named ChainA and ChainB from the corresponding chain selections in SAMSON.
When adding each group, select the chain in the Document view, use Generate based on current selection in document, give the group a clear name, and add it to the list. Then use the group’s selection-string check to confirm that it selects the intended nodes. This quick verification is worthwhile: a perfectly specified pulling direction cannot compensate for a group that contains the wrong atoms.
3. Keep the reference group in place
During production, the example restrains chain B so that chain A is pulled away from a reference group that stays in place. In the production parameters, activate the position restraint for chain B. This is distinct from defining chain B as the second group in the pull coordinate: the group definition tells the pulling setup which groups to use, while the restraint is what keeps the reference chain from moving freely during the run.
For the pull coordinate, add a COM pulling group and use the example settings: type umbrella, geometry distance, group 1 chain A, group 2 chain B, and start enabled. Set the direction to N N Y for z, 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 corresponds to 5 nm over 0.5 ns, matching the example’s production duration.
4. Treat the run as a sequence, not a single button
The pulling setup comes after preparing and minimizing the system and performing NPT equilibration. In the example, the system is prepared with AMBER03 and TIP3P water, neutralized with Na and Cl ions, and given an additional 100 mM NaCl. During equilibration, chain position restraints are enabled, and the temperature is set to 310 K. Use the wizard’s auto-fill control to carry the output of each completed stage into the next stage, then check the relevant parameters rather than assuming every setting is appropriate for a new system.
After production, inspect the trajectory and the generated pull-coordinate and pull-force plots. They help you check how the displacement and force evolve during the run. The resulting pulling data can be used as a starting point for umbrella sampling; it does not replace checking that the system, coordinate, and sampling plan suit your scientific question.
For the full sequence and interface details, see the GROMACS Wizard COM Pulling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.