When running molecular dynamics simulations—especially in a coarse-grained (CG) setup using the MARTINI force field—preparation is key. One often overlooked but crucial step is ensuring your system is properly neutralized and has the right salt concentration. This blog post walks you through how to prepare a CG system with ions using the GROMACS Wizard in SAMSON.
Whether you’re studying protein folding or assessing interactions in a membrane system, skipping the right ion setup can lead to inaccurate electrostatics, convergence issues, or even simulation crashes. Here’s how to avoid that.
Why are ions important?
Ions help neutralize the system’s net charge and replicate physiological conditions—especially important for biological systems. In coarse-grained models, where the resolution is reduced, careful setup becomes even more important due to the approximated nature of interactions.
When and how to add ions with GROMACS Wizard
After loading your CG model (usually prepared using the Martinize2 Extension for MARTINI), and setting up your system’s solvent box, GROMACS Wizard allows you to add ions in just a few steps.
- Enable solvation first: To add ions, you must first add solvent to your system. This is because ions are introduced by replacing solvent molecules.
- Check ion addition options: Under the solvation section, enable “Neutralize / Add additional ions”. You’ll be prompted to define the types of positive and negative ions (typically Na+ and Cl-).
- Specify salt concentration: If you’re aiming to mimic a physiological setup (e.g., 0.15 M NaCl), provide the desired molar concentration. GROMACS Wizard then calculates how many ions are needed.
- Proceed with preparation: Click Prepare, and GROMACS Wizard handles the rest—ions are added by replacing solvent molecules to maintain the system’s volume.
Tips for successful ion addition
- Always solvate first: Remember, without solvent, no ions can be added.
- Avoid overlaps: Adjust van der Waals distances in solvation settings to prevent overlaps when ions are inserted.
- Review ion placement: After preparation, inspect the system to ensure ions are evenly dispersed and not clashing with key molecular regions.
Ion addition might seem like a side task, but it ensures accurate electrostatics and system stability. With GROMACS Wizard in SAMSON, it integrates seamlessly into the Prepare tab workflow.
To learn more, visit the full tutorial: Coarse-Grained Systems in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.