Molecular simulations often rely on enhanced sampling techniques to capture rare events or transitions. One such method is Umbrella Sampling, widely used to estimate free energy profiles along reaction coordinates. However, a common challenge many molecular modelers face is determining how to select appropriate initial conformations for umbrella sampling simulations.
In this post, we focus on a practical and often overlooked part of the process: selecting and preparing initial conformations from an existing GROMACS trajectory using the GROMACS Wizard in SAMSON. If you’ve previously completed simulations like COM pulling, you can leverage that trajectory directly to kick-start your umbrella sampling workflow.
Why is this step important?
The accuracy of umbrella sampling largely depends on the diversity and distribution of initial configurations across the reaction coordinate. Poor choices here can lead to inefficient sampling or biased free energy estimates.
The Process in SAMSON
Once you’re in the GROMACS Wizard, simply switch to the Umbrella Sampling tab. Start by choosing an input project that contains your trajectory — this is usually a previous COM pulling simulation. SAMSON will automatically detect the trajectory file for you.
Next, define your reaction coordinate by selecting two index groups. These typically represent molecular groups between which you want to measure distance, like two protein chains or residues:
Once the reaction coordinate is defined, a plot appears showing the distance over time. SAMSON visualizes suggested initial conformations along this coordinate, helping you decide on spacing.
Choosing Initial Conformations
You have two main spacing strategies:
- Number of conformations: Specify how many conformations you want. They’ll be selected evenly across the reaction coordinate.
- Minimum COM spacing: Set a minimum center of mass distance. Only frames respecting this spacing are chosen.
To refine your selection, you can also limit the frame range from which conformations are chosen — useful when you know transitions occurred in a specific interval.
When ready, click Generate project. SAMSON creates a batch project folder with subprojects for each selected frame, along with a frames.ndx file mapping these selections. This structure keeps your simulations organized and ready for NPT equilibration and production MD steps.
Who is this for?
If you’ve ever run a simulation and wondered how to extract usable frames for Umbrella Sampling, or struggled to organize them into ready-to-run systems, this feature in SAMSON can save you hours of manual work. It also reduces the risk of user errors during preparation.
By visualizing your options and combining them with automated project generation, SAMSON lets you go from data to simulation-ready input in just a few guided steps — no scripting required.
To learn more about this functionality and continue with NPT equilibration and PMF analysis, visit the full tutorial: GROMACS Wizard – Umbrella Sampling.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.