GROMACS version: 2023
GROMACS modification: No
I am trying to understand how to set up a flat bottom potential and I have to admit, I am quite frustrated with the documentation. The restraint section:
https://manual.gromacs.org/documentation/2023/reference-manual/functions/restraints.html
does not even mention, in which files the parameters are specified. But it does tell me I need to specify g=5 and that I need to specify it that it’s not inverted, the force constant k, the range r, and the origin. However, the relevant documentation (https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html) for the file type only mentions g, r and k. Why is there so much text in the restraint reference but no example line how to add such a potential to a simulation?
There are no examples in the section describing the interaction functions. Maybe we should consider that for such complex cases.
Example (put in you atom index and use the right parameter values):
[ position_restraints ]
; atoms functype g r k
atom_index 2 5 0.5 1000