Hi Peter, This info has been helpful regarding how PBCs are implemented in OpenMM. No, I don't have a barostat on the system. However, as I noted earlier, I do have a layer of "fixed" atoms, i.e., atoms whose mass I set to zero. This represents a layer of gold to which the hydrocarbon chains are anc...

Thanks for the comments. We already do that. I believe it may be the bond that is leading the problem here and the restraint energy is just a consequence. I am just not sure how OpenMM deals with the bonds for more extended systems, e.g., long hydrocarbon chains, when there are periodic boundary con...

I am seeing an error that I want to attribute to atoms/molecules being translated "into" a periodic box as part of the PBCs but am unsure exactly what is implemented in OpenMM (looked through the code and it appears it doesn't translate atoms back into box). Can someone let me know how this works in...

Hello, I have been looking at the additional features for Amber-like GB models in the python interface/API. I cannot find that these are available in other languages, is that correct? If not correct, please let me know how I would access them, as I don't find them documented. I'm most interested in ...

Dear Peter, Thanks for the response. No, the eval doesn't have to be a parameter, but then its a bit messier because I need to detect and make different functions for different values of eval, which is a parameter that the user can set. I was trying to minimize the code that is necessary, but can tr...

Wipee, for whatever reason CUDA platform is now recognized on Mac Osx 10.9, which is wasn't in 6.0 beta. This makes me happy because I can continue developing on my laptop! Peter, sorry I didn't see your message under the Mavericks post and hence didn't try it for you. As noted above, things now wor...

Dear All, In implementing more of CHARMM's functionality through the CHARMM/OpenMM interface we have recently run into problems with some code that was written to provide the CHARMM resd restraints through CHARMM/OpenMM. The implementation uses the CustomCompoundBondForce and throws errors by produc...

Dear Peter, Thanks for the suggestion. The problem appears to be: python Python 2.7.5 (default, Aug 25 2013, 00:04:04) [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from simtk.openmm import * >>> Platform.l...

The CHARMM force fields and a growing amount of CHARMM's capabilities are available through the CHARMM/OpenMM interface we introduced a couple of years ago. This doesn't preclude moving the latest parameter/RTF files over to XML for support through the python interface, but just wanted you to know t...

Dear All, Have now verified on a new, clean MacBook Pro (15" Retina display Quad core Intel I7) with NVIDIA GT750M GPU that OpenMM5.2 and OpenMM6.0 do not work with CUDA on platforms Mavericks (OSX 10.9) running the latest Xcode (5.02) and CUDA ToolKit/Drivers from cuda-mac-5.5.28_10.9_64.pkg. While...