A reaction-coordinate pathway can show how two parts of a molecular system move relative to one another. But a pathway alone is not the set of simulations needed for umbrella sampling: you also need starting conformations distributed along that coordinate. Choosing them by hand can be tedious, and inconsistent spacing can leave parts of the pathway under-sampled.
GROMACS Wizard can turn a GROMACS trajectory into a batch project of umbrella windows. The key is to treat this as a sequence of distinct decisions: choose the coordinate, decide how to sample the trajectory, then use the same coordinate definition in equilibration and production.
1. Choose where the window conformations come from
If you already have a GROMACS trajectory—for example, from a COM pulling simulation—you can use it to select initial conformations. In the Wizard, open the Umbrella Sampling tab, select the input project, and choose two index groups to define the reaction coordinate. The resulting plot shows distance versus time, with suggested conformations marked along the pathway.
If your conformations or pathway already exist in SAMSON, there is another route: use the batch-computations workflow through NVT equilibration, then add the umbrella-specific COM pulling parameters for the later NPT and production steps. The useful distinction is simple: a trajectory is one possible source of window starting states, not a requirement.
2. Select spacing that fits your pathway
The Wizard offers two ways to choose conformations from a trajectory:
- Number of conformations: choose how many windows to create. The selected conformations are distributed evenly along the reaction coordinate.
- Minimum COM spacing: specify a minimum center-of-mass distance between selected conformations.
These controls answer different planning questions: “How many windows do I want?” versus “How far apart should neighboring starting conformations be?” You can also restrict selection to a start and end frame. That is useful when only part of the trajectory is relevant to the coordinate range you intend to analyze. Check the plotted suggestions before generating the project so you can confirm that the selected frames cover the portion of the pathway you care about.
Click Generate project to create a timestamped batch-project folder with the _umbrella suffix. Each subfolder represents one umbrella window, and frames.ndx records the original trajectory frames selected. That record helps connect each generated window back to its source frame.
3. Keep the coordinate definition consistent
Window generation is only the setup. For the batch project, run NPT equilibration and then production molecular dynamics. In both steps, add the COM pulling parameters for the reaction coordinate you plan to analyze. The tutorial’s example uses the distance between the centers of mass of chains A and B, with an umbrella-type coordinate and a force constant of 1000 kJ mol-1 nm-2.
A detail that can be easy to miss: the example sets the pulling rate to 0 nm/ps. The rate is zero so the simulation does not continue pulling the groups; the umbrella restraint parameters are still specified. The listed distance direction is N N Y, corresponding to pulling in the z-direction in this setup. Set the groups and coordinate to match the system and analysis you intend to perform; the example values are not a universal prescription.
When launching a batch project locally, the Wizard adds a separate job for each subfolder. You can monitor and manage those jobs in the Local jobs window. After the umbrella simulations finish, continue to PMF analysis, where the documentation describes computing the potential of mean force using WHAM.
The practical takeaway: decide on your coordinate and pathway range before generating windows, inspect the proposed frame selection, and carry the same coordinate definition through equilibration and production. For the complete workflow, see the Umbrella Sampling tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.