When setting up molecular dynamics simulations, a common obstacle for many molecular modelers is ensuring that simulation inputs are correct and properly referenced. This becomes particularly crucial during the equilibration phase, where one wrong file can cost time and resources.
Fortunately, the GROMACS Wizard Extension in SAMSON helps streamline this process. This blog post focuses on a key aspect of simulation setup: selecting and managing the input files needed to launch an NVT Equilibration step.
What’s the challenge?
After energy minimization, users often proceed to NVT Equilibration to bring the system to the target temperature. But if the wrong input is chosen—say, a structure that hasn’t been minimized—GROMACS may crash or return non-physical results. Navigating between simulation steps and organizing the right files can become a source of frustration, especially in longer workflows or batch simulations.
How GROMACS Wizard handles input selection
GROMACS Wizard makes it easier by offering multiple ways to select input structures for NVT Equilibration:
- GRO File: You can provide the path to a
.grofile generated from the previous step, such as the minimized structure. - Batch Project: Alternatively, supply the path to a whole project folder that contains results from a previous run, especially useful if you are working with batch computations.
To simplify this further, there’s an auto-fill button (
) that pulls in the last used file. This can be a major time-saver when working through multiple steps where continuity in data is essential.
Still want to manually specify the file? Just use the … button to browse and select your input.
Use Case: Continuing a simulation
Let’s say you just completed the energy minimization step. When you move to NVT Equilibration, just one click on the auto-fill button tells the wizard to reuse the latest successful output. This simple action ensures file consistency and continuity—a key factor in avoiding simulation errors.
Why is this helpful? Because molecular dynamics workflows often consist of several chained steps. Losing track of which file was used where—especially when projects span dozens of folders—can lead to mismatched or corrupted simulations. Having an automated and visible connection between steps reduces this cognitive load.
Also worth noting: if you’re returning to a project after some time, SAMSON remembers your modified parameters and paths. It’s all saved between sessions, which helps jump straight back into your work without retracing steps.
Tip: Working in batches
If you’re using batch mode, make sure the project you select was already minimized or prepared appropriately. Refer to the Batch Computations documentation for step-by-step guidance.
To learn more about this part of the workflow and how to launch simulations directly, view the full NVT Equilibration tutorial in the SAMSON docs: 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.