Starting a molecular dynamics simulation can feel like a chain of unrelated setup tasks: prepare a structure, choose a model, add solvent, minimize, equilibrate, and finally run production dynamics. The difficult part is often not any single step—it is knowing what needs to happen first, and which tasks depend on earlier work.
GROMACS Wizard brings these workflows into SAMSON and includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started. If your workflow requires it, the extension can also use a custom local GROMACS installation. The sequence below offers a practical way to orient yourself before beginning.
Start with the structure, not the production run
A useful way to avoid getting lost is to treat simulation as a progression of prepared inputs. First, inspect and prepare the starting molecular system. Then define the simulation setup, relax the system, equilibrate it, and only after those stages run production molecular dynamics. This order is the recommended path in the GROMACS Wizard tutorials:
- Pre-processing: load and prepare the starting molecular system before setting up GROMACS.
- Prepare: define the model, simulation box, solvent, ions, and output files.
- Energy minimization: relax the prepared system before equilibration.
- NVT equilibration: equilibrate temperature at constant volume.
- NPT equilibration: equilibrate pressure and density.
- Production molecular dynamics: run the production simulation and inspect results.
The practical benefit of following the sequence is that each stage has a clear role. If you are troubleshooting, it also gives you a sensible place to look: confirm that the system is prepared before moving to simulation setup, and complete the earlier stages required by the task you want to run. The tutorials use the 1AKI structure as an example, but the same route can be applied to your own systems.
Choose the branch that matches your system
Not every project is a standard protein-in-solvent setup. A protein-ligand complex, a coarse-grained model, or a system with a particular periodic box may need additional preparation. It is usually easier to identify these requirements before beginning the core sequence than to discover them after preparing inputs for a different kind of system.
- For a ligand complex, see Protein-ligand systems, which covers ligand parametrization and combining it with a protein.
- For box selection and minimum-image constraints, see Periodic boundary conditions.
- For coarse-grained preparation, see Coarse-grained systems.
More advanced tasks can also be planned as a separate branch. The tutorial family covers center-of-mass pulling, umbrella sampling, and potential of mean force analysis. For example, the COM pulling and umbrella sampling tutorials address workflows beyond a basic production run, while PMF analysis covers analysis after umbrella sampling.
Install once, then decide how you want to compute
To get started, add the GROMACS Wizard Extension from SAMSON Connect and restart SAMSON so the extension can be downloaded and installed. You can check for it under Home > Apps > Biology, in Interface > Preferences > Updates > SAMSON Extensions, or under User > My Extensions when signed in to SAMSON Connect.
For a project that needs repeated runs across systems or conformations, the batch computations tutorial may be relevant. If you plan to run jobs in the cloud, consult Launching computations in the Cloud. If you need a particular GROMACS installation or local performance configuration, see Using custom GROMACS version and performance parameters.
The key planning question is simple: are you following the full preparation-to-production path, or do you have a specific task with its own prerequisites? For the full path, begin with Pre-processing. For a focused task, jump to its tutorial and check what prepared inputs it requires before running it.
Explore the complete GROMACS Wizard tutorial guide to choose the next step for your system.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.