GROMACS version:
GROMACS modification: Yes/No
Hello everyone, I’m new to using gromacs. How can I prepare a peptide system in water (model TIP3P) but instead of Cl and Na ions, it has acetate ions when ionizing the system?
You will need a coordinate file of acetate to insert via gmx insert-molecules prior to solvation. You will need to manually update your system topology to include a topology for acetate and update the number of [molecules] accordingly.
thank you so much