From a Starting Structure to a Meaningful MD Run: A Workflow That Keeps Its Place

A molecular dynamics workflow can feel like a chain of unrelated setup screens: prepare a structure, choose a model, create a box, add solvent and ions, equilibrate, then run the simulation. The practical challenge is knowing what depends on what—and where to begin when you only need one part of the process.

GROMACS Wizard brings GROMACS workflows into SAMSON. It includes a compatible GROMACS build, so a separate GROMACS installation is not required to get started; if needed, the extension can also use a custom local installation. The workflow below is a useful mental map for turning a starting molecular system into a production simulation.

GROMACS Wizard in SAMSON
GROMACS Wizard provides a route through preparation, simulation, and analysis tasks in SAMSON.

Think in stages, not screens

Each stage creates a more simulation-ready version of the system. Keeping that progression in mind helps prevent a common frustration: trying to run a later task before its required inputs have been prepared.

  1. Pre-process the starting system. Begin by loading and preparing the molecular system. This is the point to make sure the structure you intend to simulate is the structure you are actually handing to the workflow. The tutorials use the 1AKI structure as an example, but the same route can be applied to your own systems.
  2. Prepare the simulation model. Define the model and set up the simulation box, solvent, ions, and output files. These choices establish the system that the subsequent simulation stages will use. If you have a protein–ligand system, consult the dedicated workflow for parametrizing a ligand, combining it with a protein, and preparing the complex.
  3. Minimize the energy. Energy minimization relaxes the prepared system before equilibration. It is a separate stage in the recommended route, rather than something to skip over on the way to production MD.
  4. Equilibrate in two steps. NVT equilibration addresses temperature at constant volume; NPT equilibration addresses pressure and density. Treat them as distinct stages with distinct purposes, and continue in that order when following the standard path.
  5. Run production MD and inspect results. Once the system has passed through preparation, minimization, and both equilibration stages, proceed to the production molecular dynamics simulation and inspect its results.

A simple way to choose your starting point

Before opening a tutorial, ask: “What do I already have, and what does the task I want to do need?” If you are new to this workflow, follow the recommended sequence from pre-processing through production MD. If your task is more specific—such as cloud jobs, custom index groups, or performance settings—you can jump directly to its tutorial. But if that task depends on prepared input files, first complete the earlier stages needed to produce them.

This small check saves time because it distinguishes a standalone configuration task from a simulation step that relies on earlier preparation. It also makes it easier to return to a workflow later: you can identify which stage is complete and which stage supplies the next set of inputs.

Branch out only when your system calls for it

The standard route is not the only route. Periodic boundary conditions guidance covers choosing box shapes and meeting minimum-image constraints during preparation. Separate tutorials cover batch computations across multiple systems or conformations, and submitting, monitoring, downloading, and importing cloud jobs. For advanced work, the tutorial family also includes coarse-grained systems, center-of-mass pulling, umbrella sampling, and potential-of-mean-force analysis.

These are useful branches, not extra steps that every simulation must take. Pick the branch that matches the system or question you are working on; keep the main preparation and simulation sequence as your reference when a task depends on previously prepared files.

Getting started

Add the GROMACS Wizard Extension from SAMSON Connect, then restart SAMSON so the extension can be downloaded and installed. If you are following a complete molecular dynamics workflow, start with Pre-processing. For the full tutorial map and links to each stage, see the GROMACS Wizard tutorials.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.

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