GROMACS version:
GROMACS modification: Yes/No
Here post your question I am new to GROMACS and would like to study the geometry of a mixed cluster consisting of 10 NH₃, 20 formic acid, and 30 phenol molecules. My goal is to obtain the geometry of this 60-molecule cluster using molecular mechanics.
I have a few questions:
- How can I generate the force field parameters for these three molecules (NH₃, formic acid, and phenol)?
- Once I have the force field parameters for each molecule, how do I merge them to set up the simulation?
- What is the process for running the molecular dynamics simulation with these combined force field parameters in GROMACS?