NPT equilibration is a critical step in molecular dynamics simulations. It’s the phase where your system stabilizes at the desired pressure and density, and skipping or misconfiguring this step can lead to inaccurate results downstream. Fortunately, GROMACS Wizard in SAMSON streamlines this process by guiding users through an intuitive interface. Still, understanding how to correctly configure inputs and pick parameters can save a lot of troubleshooting later.
In this blog post, we’ll focus on pain points many users face when setting up NPT equilibration using GROMACS Wizard: choosing the right input structure and adjusting the corresponding parameters.
Picking the Right Input Structure
This might sound simple, but users often get stuck here. The NPT step must use output from a previous minimization or NVT step. In GROMACS Wizard, you can:
- Manually specify a GRO file from a previous run
- Select a previously minimized or equilibrated batch project
If you’ve just finished the NVT step, simply click the auto-fill button to automatically propagate the path from the last successful computation. This can save time and reduce errors caused by file misplacement.
Tuning Your Simulation: Parameters That Matter
The default parameters in the Parameters section often suffice for standard systems, but it’s good practice to understand what they mean. For example, the number of steps and integration time step dictate how long your simulation runs—this affects whether your system reaches equilibrium within the given timeframe.
Typically, starting with 100 ps is recommended. Equilibration might require more depending on your system’s complexity. If equilibration isn’t achieved in one run, you can easily relaunch using the output of the previous NPT step.
Go Deeper with Advanced Options
Want full control? Open the Advanced parameters window by clicking the All… button. Here, you can customize pressure coupling, barostat settings, or temperature coupling settings. Most importantly, make sure temperature parameters align with what you used in the NVT equilibration. Mismatched settings lead to unstable or unrealistic simulations.
Position restraints (POSRES*) are pre-filled based on your input system, so generally, you don’t need to adjust them manually unless you’re doing something unconventional.
Practice Tip: Reset or Load Presets
GROMACS Wizard allows you to save and reload parameter files (.mdp) from other simulations. Just click on Load from file… or Save as… in the Advanced parameters window. This is useful if you run many similar simulations and want to ensure consistency.
Also, if something went wrong or you’re unsure what you changed, clicking Reset brings everything back to default.
Next Steps
Once your settings are ready, you can either:
- Equilibrate locally on your own PC
- Launch in the cloud if your system is large
- Generate inputs for use on an HPC cluster
After simulation, it’s important to evaluate the results: look at system density, pressure plots, and compare with expected values. If the density hasn’t stabilized, repeat the NPT step using the latest outputs.
To learn more, check the full documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/npt-equilibration/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net