Running NPT equilibration in molecular dynamics is often followed by another significant challenge: accessing and interpreting the results. For users working with GROMACS via SAMSON’s GROMACS Wizard, making sense of calculated outputs can sometimes feel daunting, especially for beginners or anyone managing multiple projects.
Fortunately, SAMSON streamlines this process with a simple and intuitive import mechanism that helps users quickly visualize and work with simulation results. Let’s walk through how SAMSON handles the process of importing results after NPT equilibration, and why it can be a helpful step towards more efficient molecular modeling workflows.
What Happens After You Launch NPT Equilibration
Once you’ve run your equilibration—whether on your local machine or in the cloud—SAMSON provides an automated follow-up. If there are no other simulations queued locally, the wizard will pop up an Import Results dialog box, allowing you to choose the best way to integrate your new data.
This small interaction provides a few helpful options tailored to where you are in your workflow:
- Import the complete simulation trajectory.
- Import only the last frame.
- Import a specific range of frames.
Fine-Tuning the Import
Rather than making assumptions, SAMSON allows you to control how periodic boundary conditions (PBCs) are treated and define what part of your system to center on—for instance, the protein at the core of your model.
Let’s say you want to evaluate system stability visually. In that case, importing the whole trajectory might be best. But if you merely need an end-state structure for further simulation or analysis, the last frame may suffice. This flexibility in import saves you time and disk space, especially when running large systems.
What if You Don’t Want to Import Now?
No pressure. If you’re not quite ready to work with the output, you can just click Cancel. SAMSON won’t discard your results—instead, they’re safely stored in the Results folder, named by launch date and step (e.g., ending in _npt for this stage).
This minimizes clutter in your workspace while still giving you access to plots and job states for later use.
Result Checking and Stability
The import process is just the beginning. SAMSON also helps you check system stability over the course of the simulation by automatically generating plots of pressure and density.
You’ll find these plots in the Plots section, offering visual insights into how your system reached equilibrium. A stable density around, say, 1008 kg/m³ for SPC/E models can confirm that your configuration is ready to move on.
Want to integrate results into another project? Just use the auto-fill feature to set the inputs from the previous NPT run and repeat or continue your workflow without repeating setup steps.
To learn more about importing results after NPT equilibration, check out the full documentation on the SAMSON website.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.