Hi Ondrej, The "undefined reference" error refers to a symbol (i.e. function name) that doesn't exist in the libraries that the compiler is trying to link against. Basically, the symbol needs to exist in the libraries for that command to work. The "clRetainDevice" sounds like a part of the OpenCL li...

Hi Esteban,

The instructions are in the user manual, under the chapter "Compiling OpenMM from source code."

Thanks,

- Lee-Ping

Hi Esteban, 1) Use the iamoeba.xml file when creating your ForceField object. When creating the System object, make sure to set polarization="direct". 2) iAMOEBA is not implemented on the OpenCL platform. The platforms that implement this interaction are Reference and CUDA. Let me know if this helps...

Hi there, It's fairly common for VDWT to become zero because the force field is attempting to fit some highly repulsive structure. For example, imagine a repulsion interaction of +30 kcal/mol (from the QM calculation); the MM calculation would typically be much higher, at perhaps +3000 kcal/mol (fro...

Hi Preeti,

Can you ask on the OpenMM forum?

Thanks,

- Lee-Ping

I'm so sorry that I missed this message! What's happening is that you are encountering a zero stdev for the reference forces, and ForceBalance is attempting to use this to normalize your force errors (to obtain a fractional error). Are you actually trying to fit your parameters to zero forces, or ar...

Some suggestions: 1) It's best if you use the most recent ForceBalance code that is downloaded straight from the GitHub repository, if you're not already doing this. 2) If the optimization is already working effectively for your problem, you may keep the liquid simulation settings -- but if you're s...

Hi Chris, Thanks for getting in touch. I think that with OpenMM, there are some defaults for the nonbonded settings which are being set in the source code, and this option isn't exposed in the input file. However, it's very reasonable that this should be an option that you can specify in running the...

Hi Ed, I don't think OpenMM supports general triclinic unit cells at the moment; they have to be orthorhombic (alpha=beta=gamma=90). The function you probably want is simulation.context.setPeriodicBoxVectors(), described here: https://simtk.org/api_docs/openmm/api6_0/python/classsimtk_1_1openmm_1_1o...

Hi Manish,

OpenMM has the anisotropic Monte Carlo barostat. I'm not sure whether the CHARMM / OpenMM interface knows how to create this object, but this documentation may be helpful:

https://simtk.org/api_docs/openmm/api6_ ... ostat.html

Thanks,

- Lee-Ping