A pulling simulation can be configured correctly in the interface and still run into a basic problem: the system does not have enough room to move in the chosen direction. Under periodic boundary conditions, a molecule that travels too far can interact with its periodic image. The box is therefore part of the pulling setup—not just a container around the starting structure.
This walkthrough focuses on the decisions that make a center-of-mass (COM) pulling setup more reliable: choosing the pulling direction, sizing and positioning the box, defining the two groups, and checking that the pull rate matches the intended displacement. The example uses the 2BEG system, pulling chain A away from chain B along the z-axis.
Start with the distance and the periodic box
Before preparing the system, write down the intended displacement and direction. In this example, chain A is pulled 5 nm from chain B along z. With periodic boundaries, the pull distance must remain less than half the box length in the pulling direction, taking periodicity into account. A box that is too short can make the intended movement incompatible with the minimum image convention.
The tutorial sets the orthorhombic box to 6.5 nm x 4.5 nm x 12 nm. The 12 nm z-length is more than twice the 5 nm pull distance, with additional space to help keep the setup suitable if part of the pulled chain extends beyond the target distance. It also sets the system center to 0.5 x 0.5 x 0.2 of the box dimensions rather than centering it automatically. In this example, that places the system away from the middle along z and leaves room in the direction of travel.
If the intended pulling direction is not aligned with a box axis, orient the structure before preparing the system. SAMSON provides object-moving tools and an alignment option in the structure’s context menu. The goal is to make the pulling axis and the box dimension used to accommodate the displacement agree.
Make the pull groups explicit
Pulling acts on index groups, so confirm that the groups correspond to the parts of the structure you intend to move. For 2BEG, the two custom groups are named ChainA and ChainB. In the index-group editor, select each chain in the Document view, generate a group from the current selection, give it a clear name, and add it to the list. You can test a group by selecting it and asking SAMSON to select the corresponding nodes in the document.
Clear names help prevent a subtle setup error: reversing the moving and reference groups. In the example, chain A is group 1 and chain B is group 2. Chain B is also position-restrained during production so it stays in place while chain A is pulled. These settings serve different roles: the index groups define the COM coordinate, while the position restraint helps keep the reference chain from moving freely.
Check the rate against the run length
The example runs production molecular dynamics for 0.5 ns and specifies a pull rate of 0.01 nm/ps. Since 0.5 ns is 500 ps, that rate corresponds to a 5 nm change over the run. Checking this simple relationship before launching the simulation helps catch mismatches between the desired displacement, the rate, and the simulation duration.
The remaining COM-pulling settings in the example are: umbrella type, distance geometry, start enabled, displacement along z (N N Y), initial distance 0 nm, and force constant 1000 kJ mol^-1 nm^-2. Together, these describe the pulling coordinate and how the pulling restraint is applied. Set the temperature and pressure coupling consistently with the NPT equilibration step, and keep chain B’s position restraint active for production.
A practical pre-run checklist
- Direction: Is the pulling axis clear and aligned with the intended box dimension?
- Space: Is the box long enough for the planned displacement while respecting the minimum image convention?
- Groups: Do the custom index groups select the intended chains, in the intended order?
- Reference: Is the reference chain restrained during production as intended?
- Timing: Does the pull rate multiplied by the run duration give the planned displacement?
After the run, inspect the trajectory and the pull-coordinate and force plots. They provide a way to review how the displacement and force changed over time. The pulling output can also be used as a starting point for umbrella sampling; it should not be mistaken for a free-energy profile by itself.
For the full 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.