A molecular structure can look perfectly reasonable on screen and still contain close contacts or awkward local geometry that make the first stages of a simulation difficult. Energy minimization is the step that helps relax these problems before equilibration—but a completed job is not automatically a successful one. The useful question is whether the structure’s energy and forces indicate that it is ready to move on.
This guide focuses on a practical workflow for checking that result with GROMACS Wizard in SAMSON. Minimization reduces unfavorable local interactions; it does not replace equilibration or prove that a system is physically realistic.
Start with the right input
Before opening the Minimize tab, make sure the system has completed the preparation step. You can provide the resulting GRO file or a prepared batch project. If you are continuing directly from the previous successful step, use the auto-fill control to populate the input path. This helps avoid accidentally minimizing an older or unrelated structure.
Keep the defaults unless you have a reason to change them
The parameters in the Minimize tab are populated with default values intended for typical energy-minimization runs. For a first pass, leaving them unchanged makes the result easier to interpret. The energy-minimization tolerance is among the settings most commonly adjusted; other GROMACS options are available through All….
If you do change advanced settings, keep track of what changed. You can restore defaults with Reset, load values from an MDP file, or save the current parameters to a file. Modified parameters are saved when SAMSON closes, so a setting changed for one project may still be present the next time you open the application.
Run the job—and keep the output
GROMACS Wizard can generate input files, run minimization locally, or launch it in the cloud. For a local run, choose Minimize locally. The Output window reports progress, and the Local jobs button lets you check job status while continuing to work.
When the job finishes, you can import the entire trajectory, just the last frame, or a selected range of frames. You can also choose periodic-boundary-condition treatment and what to center the system on. If you cancel the import, the results are not deleted; the plot is still generated. Results are saved in the configured results folder, in a time-stamped folder with the suffix _em.
Read the plot, then check the numbers
The potential-energy plot shows how Epot changes over minimization steps. A steady downward trend that levels off is a useful sign of convergence, but the plot is only one part of the check. Review the Output window for both the potential energy and maximum force, Fmax.
- Potential energy:
Epotshould be negative. For a simple protein in water, its magnitude may be on the order of 105–106, but it depends on system size and the number of water molecules. Treat this as context, not a universal pass/fail threshold. - Maximum force: Compare
Fmaxwith the target set byemtol. For example,emtol = 1000.0sets a target maximum force of no greater than 1000 kJ mol-1 nm-1.
What if the force target was not reached?
A run can reach its maximum number of minimization steps and end with a reasonable-looking energy while still having Fmax > emtol. In that case, do not assume the system is ready for equilibration. Consider why minimization has stalled. Depending on the system and parameters, possible next steps include increasing the number of minimization steps, reducing the minimization step size, or changing minimization parameters such as the integrator. You can also run minimization again using the previous minimization output as input.
The practical takeaway: use the plot to understand the trend, but use the reported energy and force together to decide whether to continue. Once both are acceptable for your system, proceed to Step 3: NVT Equilibration. For the complete walkthrough, see the GROMACS Wizard energy-minimization documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.