Force Field Selection, Solvation & Ion Placement in GROMACS

By BioDockify Computational Research Team · August 8, 2026 · GROMACS Workflow

How to choose a force field, solvate a protein system, and add ions for GROMACS molecular dynamics. Covers AMBER, CHARMM, OPLS force fields, TIP3P water, and physiological ion concentration.

Read the complete article with tables, code and references on BioDockify.

Key References

• Lindorff-Larsen, K. et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78, 1950-1958 (2010).
• Jorgensen, W.L. et al. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935 (1983).
• MacKerell, A.D. et al. All-atom empirical potential for molecular modeling. J. Phys. Chem. B 102, 3586-3616 (1998).

Scope & Limitations

Force field choice significantly affects simulation results TIP3P is a 3-site model — TIP4P may be more accurate but slower Ion parameters must match the chosen force field