A center-of-mass (COM) pulling simulation can look correctly configured and still be undermined by a basic setup mistake: not leaving enough room in the periodic box for the motion. If the pulled group travels too far relative to the box, periodic images can complicate how you interpret the separation. Planning the pulling distance and box dimensions together helps prevent that problem before a long simulation begins.
This example uses the 2BEG system in GROMACS Wizard. The goal is to pull chain A away from chain B along the z-direction, while restraining chain B. The intended displacement is 5 nm over 0.5 ns. The specific values are an example workflow, not universal settings: for another system, choose a box and pulling protocol that suit its geometry and scientific question.
Plan the box around the pull
With periodic boundary conditions, the minimum image convention matters: the pull distance must remain less than half the box length along the pulling direction. For a 5 nm pull along z, the z-dimension therefore needs to be more than 10 nm. The tutorial uses a 12 nm box length along z, adding room beyond that minimum so parts of the pulled chain can extend beyond the target displacement.
This is a useful planning check before running any calculations:
- Identify the direction in which the group will move.
- Estimate the intended displacement along that direction.
- Make the box dimension greater than twice that displacement, with additional room appropriate to the system.
- Check the system’s position within the box as well as the box length.
For the example, the box is orthorhombic and set to 6.5 nm × 4.5 nm × 12 nm. The system is not centered automatically; its center is set to 0.5 × 0.5 × 0.2 of the box dimensions. This placement is part of the example setup, so inspect the box visualization rather than assuming that a suitable box size alone guarantees a sensible starting arrangement.
Define the groups and the motion clearly
Pulling depends on selecting the intended molecular groups. In this workflow, custom index groups named ChainA and ChainB are created from the corresponding chain selections in SAMSON. Before using them, check that each group selects the expected atoms. A group-selection error can make a technically valid simulation answer the wrong question.
The example’s COM pulling coordinate is configured as follows: umbrella type, distance geometry, chain A as group 1, chain B as group 2, and the z-component enabled for the direction. The initial value is 0 nm, the rate is 0.01 nm/ps, and the force constant is 1000 kJ mol-1 nm-2. At that rate, 0.5 ns corresponds to a nominal displacement of 5 nm. Keeping the rate, run duration, and box dimension consistent is an easy way to catch mismatched settings before starting production.
Prepare and check the workflow
The example prepares the system with AMBER03 and TIP3P solvent, neutralizes it with sodium and chloride ions, and adds salt to a concentration of 0.1 mol/liter. After preparation, energy minimization, and NPT equilibration, the production run is configured for 0.5 ns with a 2 fs timestep. Chain B is position-restrained during production so it stays in place as chain A is pulled.
These preceding stages matter: pulling is not a substitute for preparing and equilibrating the system. Use the workflow’s auto-fill controls to carry inputs from one stage to the next, then review the settings that are specific to your pulling experiment. In particular, confirm the selected groups, the restrained chain, the pull direction, and the available space in the periodic box.
After the run, inspect the trajectory and the generated pull-coordinate and force plots. The coordinate plot helps you see how the separation changes over time; the force plot shows how the force develops during the motion. These outputs can also serve as a starting point for umbrella sampling, but they should be checked before being reused.
For the complete step-by-step workflow and its interface details, see the GROMACS Wizard COM pulling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.