Interactions groups for nonbonded forces

[Saugat Kandel]

I am trying to use the nonbonded forcefield in a vacuum simulation for large protein systems. In my simulations, I keep large domains of the protein system fixed in space, so there is not much point in calculating the nonbonded forces between atoms in the domains themselves. I am looking into creating an interaction group per domain. For now, I am using the NonbondedForce class, using the CutoffNonPeriodic method with the reaction field method for the electrostatic interactions. Since it doesn't look like I can create interaction groups from within the NonbondedForce class, I tried using the CustomNonbondedForce class instead, but didn't see an option there for the reaction field method. Is it possible to use the reaction field method from the CustomNonbondedForce class, or do I have to use the switching function instead?

[Peter Eastman]

Reaction field is just a minor modification to the form of the potential. It's basically equivalent to a shifting function. So you can easily create a CustomNonbondedForce using that functional form. The formula is given at http://docs.openmm.org/6.2.0/userguide/ ... ith-cutoff.

Peter

[Saugat Kandel]

I will try that. Thanks!