One challenge molecular modelers frequently face is ensuring that their system reaches a stable temperature before proceeding to production molecular dynamics simulations. This step — known as NVT Equilibration — is crucial to achieve meaningful simulation results. It sounds straightforward but can be confusing, especially when dealing with restraints, coupling groups, or the choice of simulation parameters. SAMSON’s GROMACS Wizard simplifies this process significantly.
In this post, we walk through the NVT equilibration step using GROMACS Wizard inside SAMSON, and why it could make your simulation setup smoother and more intuitive.
What is NVT Equilibration and Why It Matters
NVT equilibration is used to slowly bring your system to the desired temperature while keeping the number of particles (N), volume (V), and temperature (T) fixed. This sets the stage for later pressure equilibration and production runs. It is especially useful after the energy minimization step, as it lets the system begin to exhibit physically realistic motion.
Effortless Input Setup
The GROMACS Wizard offers a helpful feature many modelers will appreciate: an auto-fill button that automatically selects your input GRO file from the previous step. No more copy-pasting file paths or wondering whether the correct minimization output has been selected.
Tuning Parameters Without Guesswork
NVT simulation parameters are presented clearly in an accessible interface. Default values are pre-loaded — typically suitable for many systems — but can be customized easily. Key options such as the number of steps and integration time step are always visible. For finer control, click on the All… button to explore advanced parameters, including position restraints and temperature coupling settings.
Precision Control Over Temperature Coupling
Setting how temperature is distributed in your simulation is a delicate task. Should solvent and protein be coupled together or separately? The wizard gives clear options to split groups (like “Protein” and “non-Protein”) and define distinct coupling parameters. This is helpful for systems where different components relax on different timescales. Do you need custom groups? Just load the system and click Edit index groups — no command line required.
Run Locally or in the Cloud
Once everything is ready, you can launch the equilibration locally or take advantage of the cloud to offload heavy computation. For cloud runs, you’ll be asked to choose the computing resources. Regardless of your choice, progress is monitored via SAMSON’s job manager, allowing multitasking.
Visual Feedback: Has the System Stabilized?
After the run, you’re greeted by this reassuring plot showing the temperature over time:
The goal is to observe a stable plateau around your reference temperature. If not, just re-run the same step using the output of this run — a common and valid strategy in equilibration.
Organized Results and Easy Imports
Once complete, you can import results all at once or fetch specific frames. The wizard also lets you instantly center the system on your molecule of interest, apply periodic boundary condition corrections, and visualize the trajectory within SAMSON. All output files are neatly stored with clear folder names.
The GROMACS Wizard makes every portion of NVT equilibration more accessible – from setup, to monitoring, to re-running when needed. And for experienced users, it brings transparency to what would otherwise be buried in complex .mdp configurations.
To explore the full tutorial and features, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.