When running molecular dynamics simulations using GROMACS, one of the most common sources of frustration for modelers is incorrect or inconsistent input structure paths. These mistakes can easily interrupt workflows—especially during the equilibration steps, where continuity of structure and parameters matters for stability and reproducibility.
In SAMSON’s GROMACS Wizard, the NVT Equilibration step has specific expectations for what kind of input you should provide. Understanding how to properly select and auto-fill the input structure can save valuable time and significantly reduce the risk of errors.
Why input accuracy matters in NVT equilibration
The purpose of the NVT (constant Number of particles, Volume, and Temperature) equilibration step is to bring your molecular system to a stable temperature without changing its volume. This means that the input structure must come from a logically consistent previous step—typically the energy minimization or another equilibration run like a prior NVT/NPT step.
Feeding the wrong GRO file or outdated data may result in runtime errors or, worse, invalid simulation results that aren’t easily caught until post-processing.
Three simple ways to select inputs correctly
There are three main ways to specify the input structure in the GROMACS Wizard extension for SAMSON:
- Auto-fill from the previous step: This is the easiest and most reliable method. Just click on the auto-fill button
, and the path to the last successfully completed GRO or batch project is automatically populated. - Manually choose a GRO file: Click the
...button next to the input path field to browse a specific GRO file. This can be useful when you want to re-run equilibration from a non-default structure or review previous results. - Select a batch project: If your pipeline involves multiple structures or batch runs, you can load an entire batch project. This is particularly handy for workflow automation across different molecules or simulation stages.
Here’s what it looks like when you’re choosing the input:
Tips for smoother simulations
- Always start from a minimized structure. Inputs from the energy minimization step ensure that your system is geometry-optimized and free from instabilities.
- If continuing from a first equilibration attempt that failed to stabilize, reuse the GRO file from the first NVT run. This preserves temperature history and incremental changes.
- Use consistent naming conventions for output folders. The GROMACS Wizard stores results in context-aware folders (e.g., ending with
_nvt), making it easier to double-check input lineage.
Streamlining how you select input structures may not feel like the most critical step, but it’s one of those small things that can prevent larger headaches later. Equilibration relies on predictability, and that starts with choosing the right starting point.
To learn more about the NVT equilibration process with GROMACS Wizard, including parameter settings and result validation, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.