GROMACS version: 2021
GROMACS modification: Yes/No
Hi, I have a doubt regarding the simulation run of small molecule in lipid bilayer system.
I have prepared the system using Amber99 ff and it is running fine.
The total number of atoms has became very less as compared to the simulation complex of protein and ligand in water.
I have major concern with the water molecules which is less in system and the production run time has reduced drastically as compared to the run time for protein and ligand in water.
Any suggestion that I am doing it right or I am doing something wrong?