Grommp adding molecules?

GROMACS version:2022.1
GROMACS modification: Yes/No

I’m a begginner in GROMACs. I have a couple of questions regarding the GROMPP command.

I have a decanol membrane that I solvated, but for some reason, it puts water molecules within the membrane. For this reason, I had to remove them using PyMol manually.

Once the molecules are removed, I runed:

gmx grompp -f minim_steep.mdp -c $1_newbox.gro -r $1_newbox.gro -p -o em.tpr

mistakenly using the same file as before removing water molecules (*_newbox.gro is the system with no water within the membrane). But for some reason, GROMMP doesn’t complain and adds molecules within the water as if they had never been removed.

On the other side, once a correct this in the .top and run grompp as mentioned above (therefore, computing without the removed water molecules) I get the error:

ERROR 1 [file minim_steep.mdp]:
The largest distance between excluded atoms is 3.007 nm, which is larger
than the cut-off distance. This will lead to missing long-range
corrections in the forces and energies.

How can this happen if the minimization runs finely with the waters inside? Any suggestions on what could try?

I hope my explanation was not so confusing. Thanks in advance.


I am not sure I understand correctly. Do you mean that you use a topology file including more water molecules than the gro file?
In that case, grompp will give a fatal error like : “number of coordinates in coordinate file … does not match topology …”

grompp is checking if the number of atom match between topology and coordinate file. It can not add atoms or molecules.