A production molecular dynamics run is where a carefully prepared system begins generating the trajectory you want to inspect or analyze. But it is also an easy point to lose time: choosing the wrong starting file, carrying over inconsistent settings, or overlooking import choices can complicate an otherwise straightforward simulation.
A reliable approach is to treat the production step as a chain of decisions: confirm the starting state, check the parameters that must remain consistent with equilibration, choose where the job will run, and decide how you want its results brought into SAMSON.
Start from the state you actually equilibrated
Before launching, complete NPT equilibration and make sure the equilibrated system is the one you intend to continue simulating. In the GROMACS Wizard’s Simulate tab, production can start from either a GRO file from the previous step or a batch project that has been equilibrated or produced by an earlier run.
If you are continuing the previous successful step, the auto-fill button can populate the input path for you. This helps avoid manually browsing to a similarly named file or project. If you prefer, select the GRO file using the … button.
A simple habit that reduces confusion is to verify the input before touching the run settings: check that it comes from the intended equilibration or previous production job, rather than from an earlier preparation stage.
Check continuity before changing settings
The Parameters section contains commonly adjusted options, including the integration time step and number of steps. Other GROMACS options are available through All…. Defaults are provided for typical production runs, and you can modify them when your workflow calls for it.
Two groups of settings deserve a deliberate check. Temperature-coupling parameters should correspond to those used for NVT equilibration; if velocity generation is enabled, its temperature should correspond as well. Pressure-coupling parameters should correspond to those used for NPT equilibration. These checks are especially useful when loading or reusing custom parameters, since it is easy to change a production setting without noticing that it no longer matches the preceding stage.
Position-restraint options (POSRES*) are populated automatically based on the input system. For a short tutorial run, the documentation suggests resetting parameters to their defaults and setting the maximum number of steps to 50,000. That value is a tutorial choice for a quicker run, not a universal production recommendation.
In the advanced parameters window, Reset restores defaults, Load from file… imports settings from an MDP file, and Save as… writes the parameters to an MDP file. Modified parameters are saved when SAMSON closes, so if you are experimenting with settings, make a note of which values you intend to keep.
Choose the execution route that fits the job
GROMACS Wizard offers three routes: generate inputs for a project you will run elsewhere, simulate locally on your PC, or simulate in the cloud. Local simulation uses the shipped GROMACS or a version configured in the settings. Cloud simulation can suit systems that need more resources than are available locally, and requires computing credits.
For a local run, progress appears in the Output window. The job manager lets you continue using SAMSON while calculations run; use Local jobs to check the status, particularly if you have launched multiple jobs or a batch job. A progress window or warning is not itself a result—check the job state before proceeding to import.
Make result import a conscious choice
When a single project finishes and no other projects are in the local job queue, a dialog may appear with import options. If you have launched several jobs or a batch job, check their state in Local jobs. During import, dialogs offer options for the RMSD and radius-of-gyration plots, as well as trajectory handling.
You can import the whole trajectory, only its last frame, or a range of frames. You can also choose periodic-boundary-condition treatment and what to center the system on—for example, the protein. If you do not want to load the trajectory into SAMSON, clicking Cancel does not delete the results; the plot can still be generated.
The results folder is specified at the top of GROMACS Wizard. Result folders include the launch date and time and a step suffix; production MD uses _md. After completion and loading, the wizard generates radius-of-gyration and RMSD plots. Pulling simulations also generate pull-force and pull-coordinate plots. Use the figure’s Save button if you want to keep a plot as a separate file.
The useful takeaway is to preserve continuity from equilibration, choose the output you actually need, and keep the results folder in mind before launching. For the full walkthrough, see the GROMACS Wizard production MD tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.