One of the recurring confusions among molecular modelers using GROMACS is selecting the proper input files for a production molecular dynamics (MD) simulation. This seemingly simple step can quickly become a bottleneck—especially when switching between equilibration and production phases, or handling multiple batch jobs at once. Let’s clarify this with the GROMACS Wizard in SAMSON, an integrative platform for molecular design that simplifies complex workflows without sacrificing flexibility.
Why Input Selection Matters
When you complete the equilibration phase (NVT or NPT), your system finally reaches a stable temperature and density. Great! But now comes the crucial part—using this equilibrated structure as input for the production MD phase. If you accidentally select the wrong file or ignore key settings like position restraints or temperature/pressure parameters, it could invalidate hours of simulation.
Supported Input Types
To launch the production MD step in GROMACS Wizard, you need to provide one of the following:
- A GRO file generated from prior steps such as NPT equilibrium or earlier production MD runs.
- A batch project that has been through equilibration or another production MD session.
This flexibility is especially useful if you’re running dozens of simulations simultaneously. However, it also introduces the risk of accidentally selecting the wrong input source.
Auto-Fill to the Rescue
If you just completed an equilibration or MD step, there’s a quick way to port that structure into the Production MD tab: use the auto-fill button.
This button automatically fills in the path to either a GRO file or a batch project, depending on what your prior step created. It saves time and prevents manual errors, especially helpful when workflows get repetitive.
Manual Input (When You Have To)
Manually selecting a GRO file is also an option. Simply click the … button to browse and select the correct file. This is useful if you’re re-running simulations with older data or merging results from different projects.
Why This Matters Across Projects
Whether you’re simulating a small protein or a complex membrane system, having a seamless way to bridge equilibrated systems into production simulations can make a big difference. Misconfigured inputs not only waste computational resources but also your validation effort and time spent post-processing.
To learn more about setting up production MD simulations in SAMSON using the GROMACS Wizard, visit the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get it at https://www.samson-connect.net.