A production molecular dynamics run is where a prepared system begins generating the trajectory you will later inspect and analyze. Yet the transition from equilibration to production is an easy place to lose time: the wrong input may be selected, familiar parameters may not match the equilibration setup, or a completed job may leave you unsure which results to review.
A useful way to reduce those risks is to treat production as a short sequence of checks: start from the intended equilibrated system, verify the conditions that carry forward, choose a suitable execution route, and decide how you will inspect the output before launching.
Start with the system you actually equilibrated
In SAMSON’s GROMACS Wizard, production MD accepts either a GRO file from the NPT equilibration or a previous production run, or a batch project that has been equilibrated or simulated. If you are continuing directly from the previous step, the auto-fill control can populate the input path from the previous successful run. This is convenient, but still check that the selected project or file is the one you intend to extend.
This quick check matters especially when several runs or candidate systems are in play: the starting structure determines what trajectory you will produce, so confirm the source before spending compute time.
Carry forward the right conditions
The Parameters section contains commonly adjusted settings, including the integration time step and number of steps. Other GROMACS options are available through All…. Defaults are intended for typical production runs, but a default is not a substitute for checking whether the conditions match your workflow.
In particular, ensure that the temperature coupling parameters correspond to those used during NVT equilibration, and that the temperature used for velocity generation also agrees if velocity generation is enabled. Likewise, make sure the pressure coupling parameters correspond to the NPT equilibration. Position-restraint options (POSRES*) are populated automatically based on the input system.
For the tutorial, the documented exercise resets the parameters and uses a maximum of 50,000 steps so the run finishes quickly. Treat that as a demonstration setting, not a universal production length: choose the number of steps to suit the question you want the simulation to address. If you need to reuse a parameter set, the advanced parameters window can reset to defaults, load settings from an MDP file, or save them to an MDP file. Modified parameters are saved when SAMSON closes, so review them when returning to a later session.
Choose where the computation should run
There are three routes. Generate inputs creates a project you can run elsewhere, such as on a local cluster. Simulate locally runs on your PC using the shipped GROMACS or a version configured in settings. Simulate in the cloud is an option for larger systems that may require more resources than your local machine can provide; cloud launches require computing credits.
For a local run, progress is shown in the Output window, and the Local jobs control lets you check job status. You can continue using SAMSON and GROMACS Wizard while calculations run. If you launch multiple jobs or a batch job, check their state through Local jobs rather than assuming a single completion prompt will cover everything.
Make the results useful, not just completed
When results are imported, dialogs let you choose trajectory import options: the whole trajectory, the last frame, or a range of frames. You can also select periodic-boundary-condition treatment and choose what to center the system on—for example, the protein. If you cancel trajectory import, the results are not deleted and the plots can still be generated.
Two plots are generated to help inspect a production run: radius of gyration and RMSD for the selected structures, such as the backbone relative to the backbone in the initial equilibrated system. Pulling simulations also produce plots for pull force and coordinates. These plots are useful summaries to review alongside the trajectory; they are not a replacement for deciding what analysis your scientific question requires. Save a figure with its Save button when you want to keep a plot separately.
Results are stored in the configured results folder, in folders named with the launch date and time and a step suffix; production MD uses _md. Keeping track of that folder makes it easier to find the files for analysis or a follow-up run.
For the complete workflow and interface details, see the GROMACS Wizard production MD tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.