Problem in unwrap coordinates
Hello. Before about issues, thanks a lot for this great project.
I'm trying to run a simulation for molecular ionic crystals. A system consists of 288 pairs of 1,3-dimethylimidazolium cations and hexafluorophosphate anions. Graphene-like walls are used to simulate constant potential. I used CL&P force fields.
The problem is that unwrapped lammps-format trajectory shows different molecular geometry with wrapped coordinates.
However, wrapped trajectory shows octahedral geometry as intended in force fields.
It might be a problem in calculating angle potential with unwrapped coordinates. Or, my input files might be a wrong format or force field parameters are wrong.
Is there any test input files for comparing unwrapped coordinates with reference wrapped coordinates for systems with molecules? ( with harmonic angles? dihedrals? )
Thank you!
Hyungshick Park