Steered molecular dynamics can look straightforward: choose a molecular group, apply a pulling coordinate, and run a simulation. But one setup decision can undermine the whole calculation before it begins: the periodic box may not leave enough room for the molecule to travel. If the pulled group approaches its periodic image, the simulation can no longer represent the separation you intended.
This workflow shows how to plan a center-of-mass (COM) pulling simulation so the box, reference group, and pulling parameters work together. The example uses chain A of the 2BEG system pulled away from chain B along the z-axis. The same reasoning is useful whenever you are preparing a pulling calculation that may later feed into umbrella sampling.
Start with the travel distance, not just the molecule’s size
In a periodic system, a pull coordinate must respect the minimum image convention. As a practical rule, the pull distance should remain less than half the box length in the pulling direction. That means the box must be sized for the planned motion, not only for the molecule’s initial dimensions.
In this example, chain A is pulled 5 nm along z. The tutorial therefore uses a 12 nm box length along that axis: twice the planned displacement is 10 nm, with additional room to reduce the chance that parts of the pulled chain approach a periodic image. The other box dimensions are set to 6.5 nm and 4.5 nm, giving a box of 6.5 nm × 4.5 nm × 12 nm.
The system is also positioned within the box rather than automatically centered: the center is set to 0.5 × 0.5 × 0.2 of the box dimensions. This helps place the starting structure with space available in the intended pulling direction. If the pulling axis is not aligned with a box axis, orient the system first; the box dimensions and direction of travel need to agree.
Make the pulling groups explicit
Pulling depends on defining the right groups. In the example, chain A is the group being displaced and chain B is the reference. Create custom index groups named ChainA and ChainB if they are not already available among GROMACS’s default groups. In SAMSON, select each chain in the Document view, generate an index group from the current selection, name it, and add it to the list.
Check the selections before running. Selecting an index group in the group editor and asking SAMSON to select the corresponding nodes in the document provides a simple way to confirm that the group contains the chain you intend. This small check can help catch a group-definition mistake before it becomes a confusing trajectory.
Keep the reference group in place
A relative pulling experiment needs a meaningful reference. For this setup, chain B is restrained during production MD while chain A is pulled away. In the production preprocessing settings, activate the position restraint for chain B. This is distinct from choosing chain B as group 2 in the COM pulling definition: the index group identifies the reference in the pulling coordinate, while the position restraint helps keep that reference in place.
For the example, configure the COM pull coordinate as follows:
- Type:
umbrella - Geometry:
distance - Group 1:
ChainA; group 2:ChainB - Start:
yes; initial distance:0 nm - Direction:
N N Y, meaning the z direction - Rate:
0.01 nm/ps - Force constant:
1000 kJ mol-1 nm-2
The rate is tied directly to the target motion: 0.01 nm/ps × 500 ps = 5 nm. The example runs for 0.5 ns with a 2 fs timestep, so the pull rate and simulation duration are consistent. Before launching a different setup, do the same arithmetic: multiply the rate by the planned simulation time and check that the resulting displacement fits the box.
Use the output to check what happened
After production MD, inspect the trajectory and the generated pull-coordinate and pull-force plots. The coordinate plot lets you check whether the displacement developed as intended; the force plot shows how the force changed during the pull. In the example, the force builds as the simulation overcomes interactions that resist separation. These outputs are useful for reviewing the run and can also be used as a starting point for umbrella sampling.
The key preparation checks are simple: identify the two groups, restrain the reference group, align the pulling direction with the box, and verify that the planned displacement fits within the periodic geometry. For the complete workflow and interface steps, see the GROMACS Wizard COM Pulling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.