One challenge that many molecular modelers face with molecular dynamics (MD) simulations is ensuring continuity and consistency between equilibration and production runs. It may sound trivial, but mistakes in setup parameters—particularly when switching from NPT or NVT equilibrations to production—can result in simulations that look fine but yield misleading results.
Fortunately, the GROMACS Wizard in SAMSON provides a guided workflow that streamlines this transition. However, there are still a few common traps that users should be aware of when configuring production MD runs.
Setting Your Input Structure
Starting your production MD requires correctly selecting the structure from your prior step. The safest route? Use the auto-fill button, which lets you carry over your equilibrated structure automatically:
This ensures you don’t accidentally load an outdated or pre-equilibrated structure. For experienced users doing batch jobs, you can also directly select GRO files or batch projects that have been equilibrated.
Temperature and Pressure Parameter Carryover
A key point: double-check that your temperature and pressure coupling parameters match your equilibration phase. This may sound obvious, but it’s a very frequent oversight.
Important
Please ensure that the temperature coupling parameters correspond to the ones from the NVT equilibration, and the temperature in the velocity generation (if it is on) as well.
Please ensure that the pressure coupling parameters correspond to the ones from the NPT equilibration.
Modifying or Restoring Parameters
The GROMACS Wizard exposes commonly modified MD parameters—like time step and total steps—in the Simulate tab. However, sometimes you may want to revert everything to baseline defaults or load preconfigured settings from another project.
Here’s how you can manage that:
- Click Reset in the advanced parameters window to revert to defaults.
- Load from file… to import a parameter set (MDP).
- Save as… to reuse a custom configuration later.
Running the Simulation Locally or in the Cloud
You can simulate locally or, for large systems, offload to the cloud. If you’re running locally, GROMACS Wizard allows you to continue working in SAMSON while the simulation runs in the background.
Monitor progress and access your job status through the Local jobs button:
After the Simulation: What to Look For
Once the job finishes, you’ll get pop-ups to generate relevant plots, including RMSD and radius of gyration. These two are essential for quickly evaluating if your simulation appears stable and consistent.
RMSD helps you assess structural drift relative to the initial equilibrated state, and the radius of gyration gives insights into overall compactness. Save these plots and analyze them carefully before moving ahead.
By following these simple checks and using SAMSON’s GROMACS Wizard, you can reduce the chances of wasted compute time due to simulation setup issues—something both beginners and experts encounter more often than expected.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.