Molecular dynamics (MD) simulations can provide powerful insights into biomolecular behavior at atomic resolution. But running a successful production MD simulation often comes with hurdles: wrong input paths, mismatched parameters, or just extra time spent redoing steps that could have been automated.
If you’ve spent time setting up an equilibrated system in GROMACS using SAMSON’s GROMACS Wizard, the next big step is launching the production MD simulation. This is where your actual data begins to accumulate. However, many researchers struggle with ensuring that their input paths and simulation parameters are consistent with earlier steps. This post walks you through tips and lesser-known tools in the GROMACS Wizard designed to prevent setup errors and streamline your simulation launch—saving you time and effort.
Simplifying Input Selection
One common source of errors is selecting the wrong input file after equilibration. Fortunately, the GROMACS Wizard includes an auto-fill feature that can prevent manual mistakes by automatically selecting the correct path based on your previous run.
You can also manually select the input file (usually a .gro file) using the … button, but the auto-fill minimizes the risk of feeding the wrong file into your production run.
Consistency Is Key: Matching Parameters
It’s critical to ensure that the parameters of your production run match those used during equilibration:
- Temperature coupling must align with the NVT equilibration settings.
- Pressure coupling should match the NPT equilibration step.
If you’re unsure, clicking the All… button opens access to the full list of MD parameters so you can cross-check everything. This section allows direct editing, loading from an MDP file, and resetting values to defaults.
Launching Strategies: Local vs. Cloud
Depending on your system resources, you have several options:
- Simulate locally: Run the production MD on your PC using either the default or a custom-installed GROMACS instance.
- Simulate in the cloud: Offload computation to the cloud, useful for large systems. Note: This requires compute credits.
- Generate inputs only: Prepare everything for execution in an external computing environment.
Once launched, you can monitor simulation progress through the Output window and the Local Jobs interface, which remains responsive during background computation thanks to the job manager.
After the Run: Import and Analyze
Once your simulation is complete, importing results is straightforward. SAMSON guides you through RMSD and radius of gyration plots, while offering flexible trajectory import options (last frame, full trajectory, specific range, etc.).
All plots are auto-generated and stored in timestamped folders, ensuring traceability. If you’re working with Umbrella Sampling, additional plots for pull forces are also created.
By using auto-fill, parameter consistency checks, and local/cloud job management features, the GROMACS Wizard in SAMSON significantly reduces the overhead and possibility of error when moving to the production MD phase. Whether you’re running a small protein in water or setting up a membrane simulation, these features can help you stay focused on your science, not your setup.
To learn more, visit the official documentation: GROMACS Wizard – Production MD Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.