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 opportunity to relax those issues—but how can you tell whether it has done enough?
The useful answer is not just “the job finished.” Check two outputs together: the potential energy, Epot, and the maximum force, Fmax. A steadily decreasing energy plot is encouraging, but the force tells you whether the minimization met its stopping target. This small distinction can prevent a common frustration: moving on to equilibration because a run completed, then discovering that the system was not ready.
Start from the prepared project
In SAMSON’s GROMACS Wizard, open the Minimize tab after completing the preparation step. The input can be a GRO file from preparation or an earlier minimization, or a prepared batch project. If you are continuing from the previous step, the auto-fill control can populate the input path for you.
For a first pass, the default minimization parameters are intended for typical runs, so you can leave them unchanged. If you need to inspect or customize the full set of GROMACS parameters, use All…. The advanced-parameter window also lets you reset defaults or load and save parameters in an MDP file.
Watch the plot, then verify the numbers
After choosing Minimize locally, progress is available in the Output window and through Local jobs. When the job finishes, GROMACS Wizard can show the potential-energy plot. A smooth, steady decrease is a useful sign of convergence, and the plot is generated automatically when the results are loaded.
But a reassuring-looking curve is not the whole check. Read the output for both values:
Epotshould be negative. For a simple protein in water, the documentation gives an approximate order of magnitude of 105–106, with the value depending on system size and the number of water molecules. Treat this as context, not a universal pass/fail cutoff.Fmaxshould meet the target set byemtol. For example,emtol = 1000.0sets a target maximum force no greater than 1000 kJ mol-1 nm-1.
When the run ends before the force target
Minimization may reach its maximum number of steps with a reasonable-looking Epot while still having Fmax > emtol. That is a reason to pause before equilibration: the structure may not be stable enough for the next stage. Check the output rather than relying only on the fact that the calculation completed.
Possible next steps described in the workflow include increasing the number of minimization steps, running minimization again using the previous minimization output, decreasing the minimization step size, or changing minimization parameters such as the integrator. The right choice depends on the case; the key is to evaluate why the force target was not reached instead of treating the energy value alone as proof of success.
Import only what you need
When importing results, you can choose the full trajectory, the last frame, or a range of frames, as well as periodic-boundary-condition treatment and the system-centering option. For a simple check of the minimized endpoint, importing only the last frame may be sufficient. Canceling the import does not delete the results, and the plot can still be generated. Results remain in the selected results folder; minimization folders use the suffix _em.
A practical pre-equilibration check is therefore: confirm that the energy trend is sensible, verify that Epot and Fmax appear in the output, compare Fmax with emtol, and investigate any unmet target before continuing to NVT equilibration.
For the complete 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.