Before launching molecular dynamics simulations, there is a critical preprocessing step that often gets overlooked: energy minimization. This step is key to ensuring that your molecular system is stable and realistic enough to proceed with confidence. But why is it so important, and how can you do it right?
Let’s say you’ve just prepared a protein-water system in SAMSON using the GROMACS Wizard. You’re eager to simulate, but hit the Minimize button a bit too quickly. The simulation crashes or produces unphysical behavior. One of the most common culprits? Skipping or improperly performing the energy minimization step.
Why energy minimization matters
Molecular systems obtained from PDB files or initial model predictions frequently contain steric clashes or strained geometries. Running a simulation directly on such configurations can quickly lead to instabilities or errors.
Energy minimization allows the system to relax into a local minimum of the potential energy landscape. In practice, it helps eliminate unrealistic atomic overlaps and prepares your system for subsequent equilibration phases.
Getting started in GROMACS Wizard
In the Minimize tab of the GROMACS Wizard, you can load your prepared structure by either:
- Providing the path to a prepared
.grofile - Specifying a batch project path from a previous step
If you’ve just completed the preparation step, simply click the auto-fill button to populate the input field automatically.
Choosing parameters (and when to change them)
By default, SAMSON provides commonly used GROMACS parameters for minimization. These include the energy tolerance threshold, integrator type, and the maximum number of steps.
To see all parameters, click the All… button and explore advanced options.
Common adjustments include:
emtol— decrease to make minimization more stringent- Number of steps — increase if minimization doesn’t converge
- Changing the integrator (e.g. to
steeporcg)
You can reset to safe defaults at any time or load/save parameter sets from external MDP files.
Interpreting results: more than just a “done” message
After minimizing, the GROMACS Wizard not only runs the computation but also lets you inspect the outputs. Two key metrics:
- Potential energy (
Epot): Should be negative and decreasing steadily - Maximum force (
Fmax): Should fall below youremtolthreshold
If Fmax remains too high, try running the minimization again or adjusting parameters. Energy landscapes can be rugged, and some systems may need extra care.
Visualize your convergence
One feature that helps a lot is the automatic generation of plots showing the system’s energy over iterations:
This helps confirm steady convergence, or highlights if the system is stuck in a bad configuration. You can save the plot easily or compare across batch runs.
Final checks
After minimization, take a few moments to ensure:
- Reasonable energy levels
- Fmax below threshold
- Visual inspection looks clean
This preventative step can save hours of debugging later.
To explore energy minimization in SAMSON’s GROMACS Wizard in more detail, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.