A molecular structure can look reasonable and still contain close contacts or awkward local geometry that make the next simulation step difficult. Energy minimization is the cleanup step: it relaxes these issues before equilibration. But a completed job is not automatically a successful one. The useful question is whether the structure and the minimization results are good enough to continue.
Here is a practical way to run the step and interpret its most important checks in GROMACS Wizard.
Start with the right input
Open the Minimize tab and provide either the prepared GRO file or a prepared batch project. If you are continuing from a successful previous step, use the auto-fill button to populate the input path; otherwise, select the GRO file yourself. This small check helps avoid minimizing an outdated or unintended structure.
Keep the first run simple
The usual energy-minimization parameters are available in the tab, and the defaults are suitable for typical runs. For a first pass, leave them unchanged unless you have a specific reason to adjust them. Advanced parameters are available through All…; there you can reset values, load an MDP file, or save the current settings to an MDP file. Remember that modified parameters are saved when SAMSON closes, so settings from an earlier session may still be active.
Choose Minimize locally to run on your PC. You can follow progress in the Output window or later check the job through Local jobs. The job can take seconds or longer depending on the system and computer. GROMACS Wizard also offers input generation and cloud computation, but those are alternatives rather than requirements for the basic local workflow.
Do not judge success by the energy plot alone
After the job finishes, inspect the potential-energy plot. A steady downward trend is a reassuring sign that the structure is relaxing, but it is not the only test. The plot is generated after the results are loaded, and you can save it using the button above the figure.
Next, check the output for two values:
- Potential energy (
Epot): it should be negative. For a simple protein in water, the documentation gives an approximate scale of 105–106, depending on system size and the number of water molecules. Treat this as context, not a universal pass/fail threshold: values depend on the system. - Maximum force (
Fmax): compare it with the target set byemtolin the minimization parameters. For example,emtol = 1000.0sets a target maximum force of no greater than 1000 kJ mol-1 nm-1.
When the run finishes but is not ready to continue
A minimization can reach its maximum number of steps and produce a reasonable-looking Epot, yet still end with Fmax > emtol. That is a reason to pause before equilibration: the structure may not be sufficiently relaxed for the next stage. Review the output and parameters rather than relying only on the fact that the job ended.
Possible next steps include increasing the number of minimization steps, minimizing again using the previous minimization result as input, decreasing the step size, or changing parameters such as the integrator. Which adjustment is appropriate depends on the system and the cause of the remaining forces; avoid changing several settings at once if you want to understand what improved the result.
If you ran a batch project, check the results for each subproject: plots are generated for each one. For a single project, you can import the last frame or choose another range of frames. Canceling the import dialog does not delete the results, and the plot can still be generated. Results are saved in the configured results folder, in a time-stamped folder with the _em suffix.
Quick check before moving on: confirm that the energy trend is sensible, review the final Epot and Fmax, and verify that the force target is met or decide how to address it. Continue to NVT equilibration when those values are acceptable for your system.
For the full workflow and interface details, see the GROMACS Wizard energy minimization tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.