Hi all I realize that OpenMM is primarily an MD engine, but I wanted to see if I can use it for a rotamer based MC optimization. Basically for each residue I have about 1000 rotamers, and I am doing an MC in rotameric space, choosing a random residue and a random rotamer at that residue to optimize ...

Hi, I was wondering if OpenMM currently includes Debye-Huckel screening in any of its implicit solvation models?  The OpenMM manual indicates that it is possible to specify a salt concentration or Debye length when creating a system from an Amber prmtop file. Is there a way to specify either the sal...

Hi guys For the Lennard-Jones term, are the energy and force simply truncated to zero at the the cutoff distance, or is a shift/switching function applied? The manual says "optionally a switching function can be used", but I don't see that in the API anywhere (unless we are talking about using a Cus...

Thanks peter. I actually already have the force constant as a global parameter, not a per particle one. So the easiest would be to use setParameter. Thanks!

Hi guys I am using the CustomExternalForce to implement harmonic restraints, similar to https://simtk.org/forum/message.php?msg_id=4068 . I want to implement decaying restraints, by changing the force constant. Is there a way to do this aside from recreating the context each time, which seems ugly? ...

Hi all I am running an implicit solvent (GBSA-OBC) simulation of an antibody with an attached carbohydrate chain, and currently have removed the chain due to lack of parameters. Does anyone know if there are GB (radii and scale) parameters for carbohydrates? In explicit water we use the GLYCAM force...

Hi guys

I'm running a simulation of an antibody with an attached carbohydrate chain, and trying out the implicit solvent OBC-GBSA model. Are there any known GB parameters (radii and scaling factors) for carbohydrates? In explicit water we use the GLYCAM force field.

Thanks,
Sid

Thanks Peter, that worked perfectly.

Hi there I'm using Openmm-6.2, Python API. I'm trying to create a test suite form my implementation, where I want to set up my System, and then test different components of the potential energy. My ideal flow would look like this: 1. Create a System with no forces 2. Create a Context 3. Call Context...

Is there any way to know what the different parameters to addParticle exactly mean for the different GB implementations, and what their units are? Since I'm not using an AMBER parmtop file, I cant use convertParameters() and I would need to manually make sure the parameters are in the right units. I...