Center-of-mass (COM) pulling is a useful way to drive one molecular group away from another—but a setup that looks reasonable can produce confusing results if the periodic box is too short, the pull groups are wrong, or the reference group is not restrained. These details matter especially when preparing a trajectory for umbrella sampling.
This practical example uses the 2BEG system: chain A is pulled away from chain B along the z-axis. The aim is a 5 nm displacement over a 0.5 ns production run. The same planning principles can help you check your own pulling setup before launching a longer simulation.
First, make room for the pull
Periodic boundary conditions make the simulation box behave as if copies of the system surround it. In the pulling direction, the displacement must be less than half the box length, in accordance with the minimum image convention. Otherwise, the pulled group may interact with a periodic image in an unintended way.
For this example, a 5 nm pull calls for a z dimension of at least 10 nm. The tutorial adds 1 nm on each side, giving a 12 nm box length along z. The other dimensions are set to 6.5 nm and 4.5 nm, and the system center is set to 0.5 × 0.5 × 0.2 of the box size. This placement leaves room in the direction of travel rather than simply centering the structure.
If the pulling direction is not aligned with a box axis, orient the system before defining the box. In SAMSON, the structure can be reoriented with move editors or through Move selection > Align….
Define the groups you actually intend to move
GROMACS provides default index groups, but a specific protein chain may not be one of them. In the GROMACS Wizard, load the system, select chain A in the Document view, and use Generate based on current selection in document to create an index group named ChainA. Repeat for chain B and name it ChainB. Checking each group by selecting it in the document is a useful way to catch an incorrect selection before the simulation starts.
Keep the reference group in place
For this workflow, chain A is pulled relative to chain B. During production MD, activate the position restraint for chain B so it stays in place while chain A is pulled. During NPT equilibration, activate the chain position restraints shown in the tutorial. For energy minimization, the tutorial leaves the chain and water position-restraint options unchecked.
Check the pulling numbers
In the production MD parameters, add a COM pulling group and set:
- Type: umbrella; geometry: distance
- Group 1: chain A; Group 2: chain B
- Start: yes; direction: N N Y, for the z-axis
- Initial distance: 0 nm
- Rate: 0.01 nm/ps
- Force constant: 1000 kJ mol-1 nm-2
A quick unit check helps: 0.5 ns is 500 ps, and 0.01 nm/ps × 500 ps equals 5 nm. The rate and planned run duration therefore match the target displacement.
Use the output to assess the run
The example production run is 0.5 ns with a 2 fs timestep. After simulation, inspect the trajectory and the pull-coordinate and pull-force plots. The coordinate plot shows displacement along the pull coordinate over time; the force plot shows how the force changes as the system responds. These outputs can help you decide whether the trajectory is suitable for the next stage, but they do not replace checking the setup and trajectory visually.
When the pulling workflow is complete, its results can be used in umbrella sampling. For the full step-by-step procedure and related setup details, see the GROMACS Wizard COM Pulling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.