One common challenge molecular modelers face lies in achieving a stable simulation environment after initial energy minimization and temperature equilibration. Even with a minimized system at the right temperature, unstable density can still derail longer molecular dynamics (MD) simulations. Fortunately, SAMSON’s GROMACS Wizard provides a straightforward way to carry out NPT (constant Number of particles, Pressure, and Temperature) equilibration—the critical next step to achieving realistic system conditions. 🧪
This post introduces NPT equilibration using the SAMSON GROMACS Wizard—and offers a walkthrough that could save you hours of confusion when trying to achieve stable system density before production MD runs.
Why NPT Equilibration?
NPT equilibration helps systems reach the correct density by coupling the simulation box to a pressure bath. Unlike NVT (constant Number of particles, Volume, and Temperature) equilibration, the NPT ensemble allows fluctuations in volume—important for systems like solvated proteins or membrane patches where realistic density is essential.
In SAMSON, switching to NPT equilibration is done via the Equilibrate (NPT) tab within the GROMACS Wizard interface.
Smart Input Handling
You don’t need to hunt down files from previous runs. If you’re building systematically, simply click the auto-fill button (
), and SAMSON will pull the latest relevant result from your previous minimization or NVT step. Easy.
A Look at Key Parameters
In the Parameters section, you can tune values like the time step and number of steps. To reach a proper stabilization, a typical starting point is about 100 ps. Don’t be surprised if pressure or density fluctuates—physical systems do—but your goal is to see these values settle around a plateau.
If more control is needed, click the All… button to access advanced parameters—adjust barostat types, relaxation time constants, and reference pressures.
Tip: NPT parameters often work well with exponential relaxation pressure coupling and a time constant around 5 ps.
Running and Monitoring
Once configured, click Equilibrate locally to launch the simulation. Want to use cloud resources instead? That’s also an option—great for large systems, assuming you have computing credits.
While running, SAMSON allows continuous interaction with other tasks. Use the Local jobs button to monitor progress in real time.
Success = A Flat Line
Your sign of success? Flatline behavior in density and pressure plots. These are generated automatically and show how the system behaves over time.
In the example above, the density stabilizes near 1030 kg/m3, close to the expected SPC/E model value of 1008 kg/m3. If you don’t see this kind of stabilization, just re-run the NPT step using your latest output GRO file.
Final Thoughts
Stabilizing system density before moving on to full MD simulations is vital for accurate, physically meaningful results. SAMSON’s GROMACS Wizard not only guides you through NPT equilibration—it removes the friction of file handling, tuning parameters, and launching simulations.
Learn more from the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.