Running molecular dynamics (MD) simulations is just one part of the journey. Once a simulation finishes, many researchers face a more frustrating step: importing and analyzing the results. This is especially true when working with multi-step workflows like those used in pressure equilibration phases of molecular systems.
GROMACS Wizard, part of the SAMSON platform, includes built-in tools to smooth this import process. If you’ve just completed an NPT equilibrium run, here’s how to get your results—without clutter or confusion.
Automatic Import Options
If you have only run a single NPT equilibration, GROMACS Wizard simplifies everything. Once the run is complete, you’ll see a pop-up prompting you to import the results. No browsing folders. No guessing filenames. No command-line stress.
You can easily:
- Import the whole trajectory
- Import the last frame only
- Select a range of frames
And that’s not all. You can also choose the Periodic Boundary Condition treatment (such as centering) and specify what part of the system to center on, like the Protein.
What If You Ran Multiple Jobs?
If you launched several local NPT jobs or even did a batch run, things are still manageable. Click the Local jobs button to access a list of all local computations—with their state clearly displayed.
This lets you manually select the job you want to import, giving you total control over what data you bring into SAMSON. Additionally, you’re not forced to import results immediately. If you prefer to do it later, just click Cancel in the pop-up. Your results will still be available in the results folder, and plots will be generated regardless.
Where Are the Results Stored?
Every time you run a new simulation step, GROMACS Wizard creates a folder named by the launch date and time, ending with a suffix of the step name. For NPT, this suffix is _npt. You can retrieve your results later just by navigating to this folder in the results folder section at the top of the interface.
Final Tip: Reusing NPT Results
If your system hasn’t yet stabilized—say the density is still drifting—you don’t need to reconfigure everything. Simply reuse the GRO file from your latest NPT result as the input for a new run. Just hit the auto-fill button to pull in the file path, and you’re good to go for another round of equilibration.
Learn more about working with NPT results in SAMSON GROMACS Wizard by visiting the original documentation page here: NPT Equilibration with GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.