I want to define position restraints for selected atoms, where the reference position is an arbitrary coordinate. All the examples I see are to restraint atoms to their initial positions. Is there a file format to explicitly specify the reference position?
In fact the actual goal is to apply arbitrary force vectors to selected atoms, with the forces approximately constant for small changes in the atomic coordinates. Is there a better way to do that than using restraints?
To answer my own question, it looks like the ‘pulling’ feature includes an option to exert a constant force on selected groups. Looks like that will do what I intend.
The pull code should get you what you want. You can also specify a specific restraint coordinate for each particle in the system using the ‘-r’ flag in grompp. This will default to the initial coordinates if you specify nothing, which is why you have observed the behavior that you did. But you can specify other coordinates as well.