GROMACS version:2022.5-gcc-10.2.1
GROMACS modification: Yes/No
After minimizing the system energy, for calculating nvt, I faced with an error. If I set the coulombtype as PME, I receive the error "The largest distance between excluded atoms is 0.810 nm, which is larger than the cut-off distance. This will lead to missing long-range corrections in the forces and energies". While I increase the cut-off distance, I face with the error “The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist”. But if I set the coulombtype as cut-off, everything goes well. The system includes Morse type bonding, too.
Do you expect that you can have excluded interactions at a distance 0.81 nm? That is quite long.
If your structure is correct than the proper solution is to use a (slightly) larger box.
Slighlty OT, but you seem to be using a very short cut-off distance. Have you checked that that is compatible with the force field?
Thank for your response.
Indeed, I have just started to use the Gromacs and I am an amateur in it. When my cut-off (rvdw, rlist, rcoulomb) are set to 0.5 I receive the short cut-off error and If I increase them more then the 0.810, I face with the other error. I checked my topology file, it uses the “oplsaa.ff” force field. Moreover, I could not find any atoms (in bonds, angles, pairs, dihedrals and exclusions) mentioned in my topology file that have such distances. I changed my box size using the "editconf -box " command but this problem was not solved.