Deleting problematic water molecules from .gro files

User discussions
1

GROMACS version: 2023
GROMACS modification: Yes/No

Hello everyone,

I am running into an error during minimization that I know is a known issue and has been discussed before but the solutions proposed on the forum have not been able to help me find a solution.

Here is the error:

teepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =         5000
Step=    0, Dmax= 1.0e-02 nm, Epot=  4.40203e+22 Fmax=         inf, atom= 9066
Step=   14, Dmax= 1.2e-06 nm, Epot=  4.40256e+22 Fmax=         inf, atom= 9066
Energy minimization has stopped because the force on at least one atom is not
finite. This usually means atoms are overlapping. Modify the input
coordinates to remove atom overlap or use soft-core potentials with the free
energy code to avoid infinite forces.
You could also be lucky that switching to double precision is sufficient to
obtain finite forces.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  4.4020290e+22
Maximum force     =            inf on atom 9066
Norm of force     =            inf

I have tried to move the coordinates around to no success and really do not want to use soft-core potential if it isn’t absolutely necessary. I was hoping to just remove the problematic water molecule, but am unsure how to do that without messing up the .gro file. Is there a way to remove an atom from a .gro file without messing with the atom order? Maybe a way to reorder after deleting the water?

Any help is appreciated.

2

I doubt the problem is a bad water molecule. With a potential energy of 1022, something is horrendously broken in the system. It may be a coordinate problem, topology issue, or something else. I don’t think you can delete enough waters to “fix” this problem.