Running simulation with a Packmol box

User discussions
1

GROMACS version: 2021.4
GROMACS modification: Yes/No

Hello,

I am facing a problem when running a simulation with a box created with Packmol. My box has 100 molecules of water and I created a topol.top file as:

; Include forcefield parameters
#include “oplsaa.ff/forcefield.itp”

; and the SPC/E water model.
#include “oplsaa.ff/spce.itp”

[ system ]
; Name
water

[ molecules ]
SOL 100

I also created a .gro file with editconf.

However, when I try to run a simulation, I get problems like:

atom name 1 in /home/maria/Documents/simulations/water_18042024/output_files/topol.top and /home/maria/Documents/simulations/water_18042024/output_files/box.gro does not match (OW - O)

Do you know how to solve this?

Thanks!

2

The atom name and sequence in your .gro file should be same as in the .itp file.
The atom of water in spc.itp is OW, HW1 and HW2

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_116 1 SOL OW 1 -0.8476
2 opls_117 1 SOL HW1 1 0.4238
3 opls_117 1 SOL HW2 1 0.4238

So you need to adjust the .gro file.