Is there a way to perform simulations with less standard addatives?

User discussions
1

GROMACS version: 2025.4
GROMACS modification: No

Hello,
Has anyone heard of ways to model non-standard molecules such as TRIS and MOPS buffer components? As in acquire parameters.

2

There are online resources depending on the forcefield you’re using, see Protein-Ligand Complex

3

Thank you, I will investigate this.

4

One point to keep in mind is that some small-molecule parameter generators (in particular LigParGen, but I’ve seen CHARMM-GUI do it too), are not always great about the precision of their partial charge assignments. As a result, when you run a simulation with say 1 or 2 copies of the molecule everything will be neutral, but once you add enough copies of the small molecule to get a non-trivial concentration (say 0.01M or more), you’ll start running into warning from gromacs about non-neutral systems.