Hi Andresh, I would set constraints=None and use a 0.5 fs time step. Everything else looks fine to me. Let me know if this brings your result into agreement. I typically use vdwCutoff=0.9*nanometers and nonbondedCutoff=0.7*nanometers (this is the real space PME cutoff), but I don't think that should...

Yes, that sounds like the correct approach. :) When I was optimizing the iAMOEBA water parameters, I allowed the damping parameter to change (the second floating point number in the polarizability line). You might find this to be helpful. Note that the vdW and polarizability are the parameters that ...

Hi Andrish, Thanks for getting in touch. Yes, I believe this is possible. :) You would set up your calculation by deciding which force field parameters to optimize, then manually building the "targets" for fitting the parameters. ForceBalance provides some convenient modules / scripts for making tar...

Congratulations!

Hi Charles, I had issues like this when running simulations in TINKER 6.1 a couple of years ago. My solution was to apply the minimum-image convention to the displacement vector between the atom and its tethered site. It was a small change to the TINKER code and it's in the latest version (6.3). It ...

Hi Daniel,

You might be able to do this with a CustomNonbondedForce. This allows you to implement any functional form you want between any two particles without specifying that a bond needs to exist.

- Lee-Ping

Hi Daniel, Thanks for letting me know. It does sound like writing an Integrator class is the way to go, and it doesn't seem difficult although I don't know for sure. Peter is the main developer who wrote most of the code, and he can provide some helpful input. As for the intracellular and extracellu...

Hi Daniel, I think DPD in OpenMM would be very cool, but I'm not sure how straightforward it is to implement. I am not an expert in DPD, but I believe the main conceptual difference from MD or Langevin dynamics is that the random forces are acting on pairs of particles (in equal and opposite directi...

Hi Felipe, Here are some instructions for how to build and maintain the Tinker-OpenMM interface. Please read "How to Maintain". Please let me know if you have any questions. How to Build: 1) Build and install OpenMM 6.1. If building from source, enable the option for building C and Fortran wrappers....

Hi Jason, Thanks for the explanation. :) I believe Ondrej was using the NVidia drivers and corresponding OpenCL from the Ubuntu repository. It is probably a version problem then - I would recommend installing the latest NVidia driver and corresponding OpenCL from the NVidia website. As an aside, ins...