When running molecular dynamics simulations using GROMACS, selecting the right input for each step is more than a technicality—it influences the reliability of your results and the ease of your workflow. If you’re using the GROMACS Wizard Extension in SAMSON, one key moment that often raises questions for new (and experienced) users is the NVT Equilibration input selection.
After performing energy minimization, it can be tempting to rush into equilibration. However, missing a small detail—like a misconfigured input file—can force you back to square one. Here’s what you need to know to choose the right input and avoid common headaches. 🧠
Selecting Your Input
The NVT Equilibration step prepares your system at a constant number of particles, volume, and temperature, helping it reach thermal equilibrium. Before diving into this step, the GROMACS Wizard requires either:
- A GRO file (from a previous step like energy minimization or earlier NVT runs)
- Or a batch project that’s already been minimized or equilibrated
If you’ve just completed energy minimization, the easiest route is to click the Auto-fill button next to the input path field. This populates the path with the most recent valid file or batch project—no need to spend time digging through folders.
Prefer full control? Click the … button and manually pick your GRO file from a different simulation or project. This can be useful if you previously ran multiple simulations and want to cherry-pick the one with the best minimization profile.
Why It Matters
Using the incorrect or outdated GRO file can lead to misleading simulation dynamics, or in the worst case, failed runs. Since equilibration sets the stage for production MD simulations, it’s crucial the structure reflects your minimized, chemically valid system.
Batch projects offer advantages too. They often bundle more metadata and streamline reruns, especially for automation or cloud processing. If you plan repeatable workflows or large parameter sweeps, consider using a batch project as input.
Tip for Efficient Workflows
If you’re frequently switching between simulation steps, take advantage of the auto-fill and structure loading features. After loading the input structure, you can also define index groups directly from the interface—useful for advanced coupling options in temperature settings.
And remember, NVT isn’t the end of equilibration—it’s followed by NPT equilibration to stabilize the system’s density. Starting right means finishing faster. 🔁
For more tips on how to handle input selection and proceed with NVT equilibration in SAMSON, check the full tutorial here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/nvt-equilibration/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.