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Dear OpenMM developers,

Is there a way to construct a positional restraint with the reference position changing based on the system dimensions (in NPT ensemble)?
For example, if I want to apply a restraint that maintains an atom at the center of a system, how should I construct the CustomExternalForce?

Thanks,
Jumin

How about this. Put a dummy atom at the reference position. Set its mass to 0 and its charge and epsilon to 0. That way nothing should affect it except the barostat, which should scale its position with the box. Then you can add a bond between the real atom and the dummy atom.

Thank you for the suggestion.
So, are you suggesting to use CustomBondForce?
However, if I apply a bond restraint between dummy and real atom, the position of dummy can be affected by the restraint force?

Oh... The position of dummy atom may not be affected because mass is zero?

Right. You can use CustomBondForce, or just HarmonicBondForce if you want the restraints to be harmonic.

Peter, it all sounds straightforward, but when I tried to define dummy atoms and adding the bonds I got lost. Could you show an example how to do what you are suggesting? I have about 100 CA atoms that I'd like to restrain, though, not just one.

Many thanks,

Istvan

Where are you getting lost? You add the bond just like any other bond. For example,
where force is a HarmonicBondForce. If the dummy atoms have their masses set to 0, the bond force won't cause them to move.

Sorry, I am embarrassed to say but I don't know how to add a dummy atom.

Just call
And then on the NonbondedForce, call

Thanks, Peter! I really appreciate your time, these small things are so difficult to figure out for mortals.