Thank you very much! Molecules stay almost all planar.
I have another question. Since the force field I found is used in LAMMPS, do I need to multiply the constant by two, since in LAMMPS potential expression 1/2 does not appear?
If yes, is it valid for bonds, angles and dihedrals?
This is not a quadratic potential, so there is no factor 2 involved.
Unfortunately the paper doesn’t contain formulas for the potentials, but it mentions GROMACS, so I assume the bond and angle potentials have the factor 1/2.
Summming up, I have to use the constants as they are reported, the dihedral is C O O O at 180° and funct type is 1 with multiplicty 1. Is it right?
Morever, for bond the funct type I used is correct? I’m not sure because of the units of the force constant
The dihedral is O C O O.
The units for the bond potential in the paper look to be incorrect. I assume it should be kJ/mol/nm^2.
Using O C O O 180° the molecules are completely deformed
Then we are back to that the order of the atoms likely is wrong. You would need to swap the order of e.g. the last two hydrogens. Changing 180 to 0 would also fix it.
I fixed O1 C1 O4 O3 at 180° and it worked. Thank you very much