Topology mismatch

User discussions
1

GROMACS version: 2024.1
GROMACS modification: Yes/No

Hi! I used the gmx insert-molecules function 3x to create my system, specifically 290 molecules of A, 14 molecules of B, and 23 molecules of C.

I specified this as well in my topol.top file, but still get the error of mismatch in # of atoms.

#include "forcefield.itp"
#include "ligand_atom_types.itp"
#include "eps.itp"
#include "alginate.itp"
#include "rhamnolipid.itp"

[ system ]
; Name of the system
Biofilm_System

[ molecules ]
; Compound        #mols
EPS                290
rhamnolipid        14
alginate           23
2

You say you inserted 14 molecules of B. I assume B is rhamnolipid. In the topology file it says 6 of that type.

3

Apologies, I mistyped that when posting to this forum. But even after making sure that the numbers match, there is a large discrepancy of about 6000 atoms between the topology file and the system.

4

Then you have done something else than what you say above. Do it step by step (one molecule type at a time) and see where it goes wrong.