GROMACS version: 2018.8
GROMACS modification: Yes/No
Dear Justin,
I want to evaluate a PMF using umbrella sampling for rotating an atom around a dihedral angle. For example; C1, C2, C3, C4 atoms constructed a dihedral and I want to rotate C1. Would you please give some keywords for this purpose? I know how to calculated PMF based on distance (pulling), but how can I rotating an atom (around 360 degrees) and calculate the PMF. To calculate PMF, I want to define a reaction coordinate, ξ, an angle (dihedral rotation).
Best regards,
Ganj
pull-coord1-geometry = dihedral is probably what you want but I have never used it. Hopefully someone else will share their experience.