Simulating a phospholipid in amber99sb force field

User discussions
1

GROMACS version:2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No

Hello all,
i want to simulate the phospholipid molecule using amber99sb force field. I generated the top itp and gro file from the acpype and now i want to simulate the lipid. the problem is I don’t know how to add the water model Tip3p to the system. can anyone help what are the next steps to be followed to simulate the structure.

2

Hi,
You can include the water molecule in your topology file after the description of the lipid. If you use standard amber99bs (distributed with GROMACS), you can use the following line.
#include “amber99sb.ff/tip3p.itp”
You can add water molecules in your structural file by using the tool gmx solvate
https://manual.gromacs.org/current/onlinehelp/gmx-solvate.html

\Alessandra