Setting up a steered molecular dynamics run can feel deceptively simple: choose two groups, pick a direction, and specify a distance. But there is a practical trap that can undermine the setup before the simulation even begins: the periodic box must accommodate the motion you are asking the molecule to make.
This workflow addresses that problem with a concrete example: pulling chain A away from restrained chain B in the 2BEG system. It also shows how to define the groups and translate a desired displacement and duration into a pulling rate. The goal is not just to start a run, but to make the setup easier to inspect and reuse for umbrella sampling.
Plan the box around the pull
Periodic boundary conditions make a simulation cell behave as though copies of the system repeat in every direction. As a result, a pull that is too long relative to the box can bring the moving group into interaction with a periodic image. The minimum image convention is the key constraint: the pull distance must remain less than half the box length along the pulling direction.
In the 2BEG example, chain A is pulled 5 nm from chain B along z. A 10 nm z dimension would be twice the target distance, but the tutorial adds 1 nm of extra space on each side and uses a 12 nm box length in z. The other dimensions are set to 6.5 nm and 4.5 nm. The system is positioned off-center, with the center set to 0.5 × 0.5 × 0.2 of the box, so the available space better suits the intended direction of motion.
A useful planning habit is to decide the pulling axis and target displacement first, then check the box length against the half-box limit. If the natural orientation of your system does not align with an axis, orient it before defining the box and pulling coordinate.
Make the two groups explicit
For this example, chain A is the group being moved and chain B is the reference group. In GROMACS Wizard, custom index groups can be generated from selections in the SAMSON Document view. Select chain A, generate a group from the current selection, and name it ChainA; repeat for chain B and name it ChainB. You can then test each group by selecting it in the index-group list and asking SAMSON to select the corresponding nodes in the document.
This check is worth doing before a long calculation. A correctly named group is not necessarily a correctly defined group: confirming the selection helps catch an unintended chain or incomplete selection early.
Keep the reference chain in place
The example uses a position restraint on chain B during production MD, while chain A is pulled away. This distinction matters: the pulling coordinate describes the relative motion between the two groups, while the restraint helps keep the reference chain from drifting with the moving chain. For the NPT equilibration step, the tutorial activates position restraints for chains; for production, it specifically restrains chain B.
Before production, set up the basic simulation parameters and then configure COM pulling: type umbrella, geometry distance, group 1 ChainA, group 2 ChainB, start enabled, and the z component selected for the distance coordinate. The initial displacement is 0 nm.
Check the rate against the run duration
The target is 5 nm over 0.5 ns. Since 0.5 ns is 500 ps, the required rate is 5 nm ÷ 500 ps = 0.01 nm/ps. The tutorial uses a force constant of 1000 kJ mol^-1 nm^-2. Keeping the units visible in your notes makes it easier to spot a rate entered on the wrong time scale.
The example’s production run is 0.5 ns with a 2 fs timestep. Once it finishes, inspect the trajectory and the pull-coordinate and force plots. They help you see how the displacement and force develop over time; they are also a practical check that the simulation produced the intended pulling behavior. The resulting trajectory can then be used as a starting point for umbrella sampling.
For the complete sequence—including system preparation, minimization, equilibration, and production settings—see the GROMACS Wizard COM Pulling tutorial.
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