A production molecular dynamics run begins before the first simulation step. One frequent source of avoidable trouble is a shaky handoff from equilibration: the wrong input, parameters that no longer match the equilibrated system, or results that are imported in a way that makes later inspection difficult.
This checklist focuses on those decisions in GROMACS Wizard. The aim is not to prescribe a universal simulation setup, but to help you make the next run deliberate and easier to review.
1. Confirm the system you are continuing from
Production MD should start from a system that has completed NPT equilibration successfully. Before launching, make sure that this is the system you actually want to continue simulating.
GROMACS Wizard can take either a GRO file from equilibration or an earlier production run, or an equilibrated batch project. If you are continuing directly from the previous step, the auto-fill button can populate the input path from the previous successful project. Otherwise, select the GRO file or batch project yourself.
This small check matters: the input file or project determines which structure the run continues from. If you have multiple projects or runs, verify the chosen source rather than relying on memory.
2. Treat equilibration parameters as part of the handoff
The Parameters section contains commonly adjusted values such as the integration time step and number of steps. Other GROMACS options are available through All…. Defaults are provided, but “default” does not mean every setting should be accepted without checking the context of your system.
In particular, compare the production settings with the equilibration stages:
- Check that the temperature coupling parameters correspond to those used in NVT equilibration.
- Check that the pressure coupling parameters correspond to those used in NPT equilibration.
- If velocity generation is enabled, make sure its temperature is consistent with the intended setup.
Position-restraint options are filled automatically based on the input system. For other settings, the advanced-parameters window lets you reset to defaults, load parameters from an MDP file, or save the current parameters to an MDP file. That makes it easier to distinguish a deliberate custom setup from a collection of changes you may have forgotten about.
3. Choose a run length for the purpose of the run
For the tutorial, the maximum number of steps is set to 50,000 so the example finishes quickly. Treat that as a tutorial setting, not a general recommendation for production research. Set the number of steps according to your simulation goal and workflow.
You can generate input files for use elsewhere, simulate locally, or submit the job to the cloud. Local simulation is convenient for a suitable PC; cloud computation is an option for systems that need more resources, and requires computing credits. While a local job runs, its status can be checked through Local jobs.
4. Plan how you will inspect the results
After the run, GROMACS Wizard can generate radius-of-gyration and RMSD plots. The RMSD plot depends on the structures selected for comparison, so pay attention to the plotting options when importing results. If the simulation involves pulling, pull-force and pull-coordinate plots are also generated.
Importing the trajectory is a separate choice from keeping the results. You can import the whole trajectory, only the last frame, or a selected range of frames, and choose periodic-boundary-condition treatment and what to center on. If you do not want to import the trajectory, cancelling that import does not delete the results; the plots can still be generated.
Finally, note where the results are stored: they are saved in the configured results folder, in a folder named with the launch date and time and a step suffix such as _md. Knowing this makes it easier to find the output later and use it for analysis or another simulation.
A useful pre-run habit is to check the input, compare coupling settings with equilibration, choose a purposeful run length, and decide how much trajectory you need to import. For the complete workflow, see the Production Molecular Dynamics documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.