A molecular system can finish an energy-minimization run and still not be ready for equilibration. That is a common source of uncertainty: the job has completed, the energy has dropped, and there is a plot—but what tells you whether the structure is in good enough shape to move on?
The useful answer is to check two values together: the potential energy, Epot, and the maximum force, Fmax. A smooth-looking plot is helpful, but it is not the whole story. Here’s a practical way to run the minimization and interpret its results in GROMACS Wizard.
Start with the right input
Energy minimization follows preparation in the GROMACS Wizard workflow. In the Minimize tab, select either the prepared GRO file or a prepared batch project. If you are continuing from a previous successful step, the auto-fill button can populate the input path for you; otherwise, browse to the GRO file yourself.
For a first run, the default minimization parameters are intended for typical cases, so you can leave them unchanged. The frequently adjusted settings are in the Parameters section; use All… to access the other GROMACS parameters. If you do change advanced settings, note that they are saved when SAMSON closes. You can restore defaults with Reset, or load and save settings through MDP files.
Choose how to run the job
GROMACS Wizard offers three routes: generate input files to run elsewhere, minimize locally on your computer, or minimize in the cloud. Local execution is a straightforward choice when your computer has the resources for the job. Cloud execution may suit larger systems, but it requires computing credits. For a local run, click Minimize locally and monitor progress in the Output window or through Local jobs.
Read the plot—and then check the numbers
The plot shows how potential energy changes during minimization. A steady downward trend is a useful sign of convergence, and GROMACS Wizard generates and saves the plot when the job finishes and results are loaded. Batch projects also receive plots for their individual subprojects.
Next, inspect the output for Epot and Fmax. For a simple protein in water, the potential energy should be negative and may be on the order of 105–106, depending on system size and the number of water molecules. Treat that scale as context, not a universal pass/fail threshold.
Fmax is the maximum force, and the target is set by emtol in the advanced parameters. For example, emtol = 1000.0 sets a target of no greater than 1000 kJ mol-1 nm-1. Check the final output value against the target you chose. A reassuring energy value does not, by itself, mean the force target was reached.
If the force target was not reached
A minimization can use all its allowed steps and end with a reasonable Epot, yet still have Fmax > emtol. In that situation, pause before proceeding to equilibration: the system may not be stable enough for the next stage. The documentation suggests evaluating the cause and considering more minimization steps, a smaller step size, or different minimization parameters, such as the integrator. You can also run minimization again using the previous minimization result as input.
When results are ready, choose whether to import the full trajectory, its last frame, or a range of frames. You can also select periodic-boundary-condition treatment and what to center the system on. If you cancel the import, the results are not deleted and the plot can still be generated.
A quick readiness check: confirm the job finished, review the energy trend, find the final Epot and Fmax in the output, and compare the force with your emtol target. Continue to NVT equilibration only when the energy and maximum force are acceptable for your system.
For the full workflow and interface details, read the Energy Minimization tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.