When preparing molecular dynamics simulations, one of the most common sources of confusion is choosing the correct input for each stage of the simulation pipeline. This is especially true when transitioning between the NVT and NPT equilibration steps. If the starting structure isn’t correctly selected, things can go wrong quickly—bad trajectories, missing atoms, or non-physical densities can result, wasting time and computing resources.
In the GROMACS Wizard integrated into the SAMSON platform, the interface is designed to help guide users smoothly through each equilibration step. However, understanding how to choose the correct input files for NPT equilibration can make or break a simulation.
Understanding Your Input Options 🔍
When starting an NPT equilibration run, GROMACS Wizard expects you to supply either:
- A .gro file (GROMACS structure file) from a previous step: minimization or NVT equilibration.
- A batch project that includes previous equilibration data.
If your simulation followed the expected pipeline (i.e., minimization → NVT → NPT), then the Wizard simplifies the process. Just click the auto-fill button and it automatically retrieves the correct path to the output file from the previous step:
This ensures seamless continuity, and prevents potential mistakes from manually selecting the wrong file version. But sometimes this auto-fill option may not be applicable—especially when you want to rerun NPT using outputs from custom settings or a different trajectory snapshot. In such cases, you’re free to browse for the specific .gro file by clicking the … button. Just make sure that:
- The file has all atoms present and appropriately named.
- It corresponds to the exact state of the system you wish to use (e.g., minimization or NVT output).
Why Input Selection Matters
Choosing an inappropriate file—say, one that’s too early in the pipeline—can result in numerical instabilities or inaccurate pressure and density values. These issues often appear only after running time-consuming simulations, so they’re best avoided up front. This is why SAMSON’s GROMACS Wizard includes visual indicators and file organization based on timestamps and simulation stages (e.g., folder suffix _npt).
What to Do if the Density Is Off
Not seeing the expected density after your NPT run? You can simply rerun the NPT equilibration using the output from the previous NPT run. No need to go back to NVT or minimization. Just click the auto-fill button again to use the most recent output:
This practice of restarting from a previous equilibration helps ensure that your system reaches the desired physical state before moving on to production simulations.
In Summary
Correct input file management can save hours of computation and ensure the physical integrity of your simulation. The GROMACS Wizard makes this easier by automating file tracking and providing clarity in file selection—whether you’re continuing from NVT, rerunning NPT, or loading custom setup files.
đź“– Learn more from the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.