When a molecular system is ready for simulation, a steep energy curve can feel reassuring. But a plot that appears to settle down does not, by itself, tell you whether the structure is ready for equilibration. Energy minimization is meant to relax steric clashes and poor local geometry; checking both the energy and the maximum force helps you decide whether that job is complete.
Here is a practical way to run and assess this step in SAMSON’s GROMACS Wizard, with an emphasis on what to look at before moving on.
Start with the prepared system
First complete the preparation step and keep its project folder available. In the GROMACS Wizard, open the Minimize tab. You can provide either a GRO file from preparation (or a previous minimization) or a prepared batch project. If you are continuing from the previous step, the auto-fill button can populate the input path from the previous successful run.
For a single structure, choose the GRO file directly or use auto-fill. For multiple conformations, the same workflow can be used with a batch project. This small input check is worth doing carefully: minimization should start from the prepared system you intend to continue with.
Keep the first run simple
The Parameters section contains commonly adjusted settings, including the energy minimization tolerance. Other GROMACS parameters are available through All…. For a first run using this tutorial, leave the defaults unchanged. If you do need custom settings, the advanced window lets you reset defaults or load and save parameters in an MDP file. Modified parameters are saved when SAMSON closes, so remember that a later session may retain your previous choices.
Choose where the calculation runs
GROMACS Wizard offers three options: generate project inputs, minimize locally, or minimize in the cloud. For the local tutorial workflow, click Minimize locally. Progress and messages appear in the Output window, and the Local jobs button lets you check the job’s status while calculations run. Cloud computations require computing credits; generating inputs can be useful when you plan to run the project elsewhere.
Read the result, not just the curve
After the job finishes, the wizard can offer import options. You may import the whole trajectory, only the last frame, or a selected range, and choose periodic-boundary treatment and what to center the system on. For example, importing only the last frame and centering on the protein is one available choice. Canceling the import does not delete the results; the plot is still generated.
The potential-energy plot, Epot, is useful for seeing how the energy changes over minimization steps. A steady downward trend and convergence are encouraging, but use the output to check two values before continuing:
- 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 value. - Maximum force (
Fmax): compare it with the target set byemtolin the advanced parameters. For example,emtol = 1000.0corresponds to a targetFmaxno greater than 1000 kJ mol-1 nm-1.
A minimization can reach its maximum number of steps and still end with a reasonable Epot while Fmax remains above the target. In that situation, do not treat a reassuring-looking energy value as proof that the system is ready. The documentation suggests evaluating the cause and considering more minimization steps, a smaller step size, or different minimization parameters. You can also use the previous minimization output as the input for another run.
When both values are acceptable for your system, continue to NVT equilibration. For the full workflow and parameter details, read the Energy Minimization tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.