MD simulation of charged ligand

User discussions
1

GROMACS version:
GROMACS modification: No

Hello everyone,

I am working on a molecular dynamics simulation involving a ligand that has a charged nitrogen atom. I would like to confirm whether GROMACS takes formal charges into account during the simulation. Does the software directly utilize the formal charges defined for the molecule, or are these charges determined based on the topology file or force field parameters used?

Thank you in advance!

Best regards,
Marusya

2

The partial charges are specified in the force field parameters for the ligand. So make sure that the formal charge is taken into account when you set/generate the ligand parameters. If the ligand has a formal charge of +1, you should check that the partial charges of it sums to 1. The charges are distributed, so you should not expect an integer charge of +1 on the nitrogen atom.

3

Got it, thanks a lot!