Using 4-point water model

User discussions
1

I want to run a simulation with Amber bsc1 FF with OPC water model.

I found out that OPC cannot be used directly so I initially started with tip4p and then manually changed to OPC in the topology file.

I used the following commands:
gmx_mpi pdb2gmx -f dna.pdb -o dna.gro -water tip4p

gmx_mpi editconf -f dna.gro -bt octahedron -d 1 -o boxed.gro
gmx_mpi solvate -cp boxed.gro -o solv.gro -p topol.top
gmx_mpi grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

However, there is a mismatch between the solv.gro and topol.top file which I figured out was due to the topol.top calculating for a 4-point model but the actual .gro file contains 3 atoms per molecule of water. How to solvate with the 4-point model?

2

This is because you don’t specify any solvent type ingmx solvate and so by default GROMACS uses a 3-point water model. You can specify a 4-point one with the additional flag -cs tip4p.gro.

3

Thank you for the response! I found the file and will implement it accordingly.