For many molecular modelers, setting up coarse-grained (CG) molecular dynamics (MD) systems can be a tedious and error-prone task. Between topology generation, solvation, ion addition, and force field configuration, it’s easy to get stuck in a series of manual steps that slow down scientific progress.
If you’re working with soluble proteins and need to quickly move from a CG model to a ready-to-run MD system, the GROMACS Wizard Extension in SAMSON might be what you’re looking for. Here’s a hands-on guide to walk you through the setup process using a CG model generated with Martinize2 and the MARTINI v3.0.0 force field.
From Folder to Simulation-Ready Structure
Begin by switching to the Prepare tab of GROMACS Wizard and selecting your system using:
- Set system > From > Folder
Browse to the folder where your Martinize2 outputs (like *_CG.top and *_CG.pdb) are stored. SAMSON automatically detects all relevant files:
Box and Force Field Configuration
Next, load the CG structure to compute the periodic box dimensions. This automatically generates a properly-sized simulation box for your system:
If you’re using the MARTINI model, the wizard will detect this and use the built-in martini_v.3.0.0 force field and appropriate water model:
Proper Solvation for CG Systems
One common pitfall in CG simulations is improper solvation. By default, GROMACS applies a van der Waals distance that may be too small for CG beads (especially Martini water beads). Change it to a safer distance like 0.21 nm by clicking the gear icon under Add solvent:
Fine-Tune Your System
You can tweak the periodic box by changing the box type to a Rhombic dodecahedron and setting a minimum wall distance of 1 nm. If needed, add ions to neutralize or simulate a specific salt concentration. This step requires solvent to be added, since ions displace solvent molecules.
Finalizing the Preparation
Once configured, click Prepare. The structure will be processed, and you can inspect the output visually. SAMSON automatically colorizes water (blue) and ions (using CPK colors) for easy identification.
This streamlined process not only reduces time and manual effort—it also helps maintain consistency in CG model setups. For researchers dealing with repeated runs or needing to process multiple proteins, having a visual, guided, reproducible path from MARTINI outputs to simulation-ready systems within the same environment can save hours.
To explore the complete tutorial or dive into advanced steps like minimization and equilibration, visit the full documentation at:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/coarse-grained-systems/
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.