When preparing molecular systems for simulations, many researchers overlook a crucial step: neutralizing the system with the proper concentration of ions. This step is simple but can save you hours of troubleshooting down the line when your simulation produces unexpected behavior or fails to converge.
Why is neutralization necessary?
Most biomolecular systems, especially those derived from PDB files, possess a net charge. Molecular dynamics software like GROMACS expects the system to be overall neutral to accurately compute long-range electrostatics with algorithms like PME. Neglecting this may lead to artifacts in your output or instabilities in pressure and energy during the simulation.
How SAMSON makes it easy
Using the GROMACS Wizard in SAMSON, you can neutralize your system in a few clicks. Here’s how it works in the COM pulling tutorial (but the principle applies to any system).
1. Choose your ions
In the “Prepare” step of GROMACS Wizard, select the options to include Na+ and Cl– ions. These will be used both to neutralize your system and optionally to simulate a salt environment.
2. Activate neutralization
Make sure the Neutralize system option is checked. SAMSON will calculate the total charge of your system and add the corresponding number of counterions to bring the charge to zero.
3. Add physiological salt concentration
Activate the Add additional ions option and choose your salt concentration. In the tutorial, 100 mM NaCl is added, which closely mimics physiological conditions. Specify Salt concentration and input 0.1 mol/liter.
Why not just let GROMACS handle it?
You could manually neutralize your system using GROMACS commands, but it typically involves calculating the system’s net charge, figuring out how many ions to add, and modifying topology files. GROMACS Wizard automates this within the graphical interface, reducing errors and speeding up the setup process.
Common mistake to avoid:
Ensure you neutralize before starting energy minimization or equilibration. Adding ions after these steps requires restarting the preparation from scratch.
Bonus tip:
After adding the ions, visualize them in SAMSON. It’s a good practice to inspect whether they’ve been placed sensibly (e.g., not too close to your protein, not clustering unnaturally). This quick check helps catch artifacts that might later influence simulation stability.
To see this step in action within the full COM pulling workflow, visit:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/com-pulling/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.