One of the most recurring challenges faced by researchers working with coarse-grained (CG) molecular systems is system preparation. When preparing CG systems for molecular dynamics (MD) simulations using GROMACS, minor parameter misconfigurations can easily lead to inaccurate results or unstable simulations. Fortunately, the GROMACS Wizard in SAMSON offers an intuitive interface to streamline this process and reduce the likelihood of errors.
Why Coarse-Grained (CG) System Preparation Can Be a Struggle
In traditional all-atom simulations, GROMACS provides strict definitions for van der Waals distances, solvation behavior, and force fields. However, CG modeling—such as with the MARTINI force field—requires different assumptions, and GROMACS doesn’t natively handle all of them smoothly. For example:
- Default van der Waals distances may cause incorrect solvent packing.
- Incorrect solute-box distances can lead to self-interactions across periodic boundaries.
- Forces and solvent models must be carefully aligned with your CG topology.
These often require manual tweaking of input files, increasing the potential for error. SAMSON’s GROMACS Wizard offers guided workflows specifically for CG systems, making these concerns easier to manage.
Key Steps to Get It Right
Let’s walk through some critical steps where the GROMACS Wizard adds real value in CG system preparation.
1. Load Your CG Structure Correctly
Start by selecting the appropriate output folder from Martinize2, which includes your *.pdb and *.top CG files. GROMACS Wizard will automatically detect and display input files:
2. Set the Right Force Field
If using MARTINI models, GROMACS Wizard will auto-select martini_v.3.0.0. Check the force field configuration and ensure it’s accurately selected. This is crucial for correct simulation behavior.
3. Solvation: Adjust van der Waals Distances
Unlike all-atom systems, CG beads represent clusters of atoms (e.g., one MARTINI water bead equals 4 water molecules). GROMACS defaults to a 0.105 nm van der Waals distance, which is too small for these beads. Adjust this to at least 0.21 nm to avoid overlaps:
4. Configure Your Simulation Box
System boundaries matter. Increase the solute-to-box wall distance to prevent self-interaction under periodic boundary conditions. The Rhombic dodecahedron shape is space-efficient and often recommended:
5. Add Ions the Right Way
Ions are added by replacing solvent molecules. Ensure you’ve already added solvent before this step, then define your ion concentrations or just neutralize the system:
Final Preparation and Beyond
Once your system is ready, click Prepare and optionally load the resulting structure to inspect it. SAMSON automatically colorizes water and ions, improving visual comprehension of your system configuration:
By following this structured preparation process, many common mistakes can be avoided, paving the way for successful and reproducible MD simulations using CG models.
Learn more in the complete tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.