Computational molecular scientists often face the frustration of simulation errors caused by incorrect or inconsistent inputs—especially during the NVT equilibration step in molecular dynamics workflows. If you’ve ever encountered unexpected results or crashes at this stage, you’re not alone. One common pitfall is not selecting the correct input structure file after energy minimization or previous simulations. Fortunately, SAMSON’s GROMACS Wizard offers features that greatly simplify and secure this step.
Let’s dive into how to efficiently select and validate input structures for the NVT Equilibration step in SAMSON, and how a few small options can save you significant debugging time later. 🧪
Use the Auto-Fill Feature Whenever Possible
GROMACS Wizard allows you to automatically reuse the output from a previous step (like energy minimization) as the input for your NVT Equilibration. This greatly reduces the risk of pointing to the wrong file or an outdated configuration.
To do this:
- Simply click on the Auto-fill button (
) next to the input field. - The path will be completed automatically from your most recent successful run—either a
.grofile or a batch project file.
This tiny feature saves time and helps ensure continuity in your simulation workflow:
Do It Manually (If You Prefer)
If you prefer full control, you can manually choose your input file:
- Hit the … button next to the input path field.
- Select the
.grofile or batch project from your file system.
This is especially useful if you have conducted multiple simulations and want to branch your workflow from a specific earlier point.
Input Requirements You Shouldn’t Overlook
By default, GROMACS Wizard expects that the input structure:
- Has undergone successful energy minimization
- Is compatible with the force field and box dimensions used earlier
Providing an incorrect or unmatched file here can silently cause downstream issues like instabilities or nonphysical behavior in temperature.
Where It Helps the Most
If you’re running batch projects or managing multiple simulation trajectories, having reliable input references is crucial. The auto-fill avoids version mismatches, incorrect directories, or typos that may otherwise derail an entire set of jobs.
Pro Tip: Preview Before You Proceed
Before launching the NVT equilibration, hit the Load button next to your file path to visualize the selected system in SAMSON. This simple visual confirmation can alert you to any last-minute errors, such as loading the wrong molecule or an unintentionally restrained system.
Reliable input selection helps ensure smoother simulations and saves hours of troubleshooting. Checking and confirming your structure early in the workflow helps avoid issues that only show up minutes (or hours) into a job.
Learn more in the official GROMACS Wizard documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON here.