A pulling trajectory can show how a molecular system moves along a coordinate, but it is not, by itself, a set of umbrella-sampling simulations. The practical challenge is turning that trajectory—or another collection of conformations—into a batch of windows, then keeping the reaction-coordinate setup consistent through equilibration and production. Here’s the workflow in plain language, with the steps that are easiest to mix up called out.
First, choose where your starting structures come from
There are two routes. If you already have a GROMACS trajectory, you can select frames from it to seed the umbrella windows. The COM Pulling tutorial is one example of how such a trajectory may be created. If your starting conformations or pathway already exist in SAMSON, use those instead; the documented route is to follow the Batch computations workflow through NVT equilibration, then add the umbrella-specific COM pulling parameters for the later stages.
This choice matters because it determines how the windows are created. The trajectory route includes a dedicated generation step in the Umbrella Sampling tab. With existing conformations, you work from the batch-computation setup rather than selecting frames from a GROMACS trajectory.
Define the coordinate before choosing windows
For the trajectory route, select the input project in the Umbrella Sampling tab. GROMACS Wizard identifies the trajectory in the project folder. Then define the reaction coordinate by choosing two index groups. In the example below, the coordinate is the distance between the centers of mass of chain A and chain B.
Take a moment to check that the selected groups correspond to the motion you actually want to analyze. The reaction coordinate is the quantity you will later examine in the PMF analysis, so group selection is not just a setup detail. Custom index groups can also be added if your simulation or analysis requires groups beyond the ones already available.
Choose window spacing with the trajectory in view
GROMACS Wizard displays distance versus time and indicates suggested initial conformations. You can choose them in either of two ways:
- Number of conformations: specify the total number, and the conformations are distributed along the reaction coordinate.
- Minimum COM spacing: specify a minimum center-of-mass distance between selected conformations.
You can also restrict selection to a start and end frame. This is useful when you want the starting structures to come from a particular portion of the trajectory, rather than from its full duration.
These controls answer different questions: the number option sets how many starting conformations to select; the minimum-spacing option sets a distance criterion. Neither choice replaces checking the plotted coordinate and the selected range. The resulting batch project contains a subfolder for each window, while frames.ndx records which original trajectory frames were chosen. That record is useful when you need to trace a window back to its source frame.
Keep the coordinate, but stop the pulling
After generating the batch project, run NPT equilibration and production MD for it. Add the COM pulling parameters for the reaction coordinate in both stages: the parameters affect the system’s behavior, so the tutorial specifically calls for them during NPT equilibration as well as production. For the example distance between chains A and B, the settings include umbrella type, distance geometry, the two chain groups, and a force constant of 1000 kJ mol-1 nm-2. The rate is set to 0 nm/ps so the setup does not continue pulling the groups during these simulations.
The example also sets the distance direction to N N Y (the z-direction) and the initial value to 0 nm. Treat these as the tutorial’s example settings, not universal values: choose groups and coordinate settings appropriate to the reaction coordinate you intend to study.
When launching locally, a batch project creates a separate job for each subfolder. You can monitor those jobs in the Local jobs window. Once the umbrella simulations are complete, continue to PMF analysis to compute the potential of mean force using WHAM.
For the full workflow and interface details, see the GROMACS Wizard umbrella-sampling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.