Peter et al., We are trying to finish up our CPHMD plugin to complement the recent implementation of the GBSW model in the CHARMM/OpenMM interface and are running into an issue that I think I ran across before but cannot find any detail of. This has to do with reordering of atoms to optimize the til...

Peter, I have researched this and apparently there is a new security measure in OSX 10.11 that disables the import of $DYLD_LIBRARY_PATH and this the path to non-OSX installed libraries, etc. are inaccessible to the application. I note I installed OpenMM 6.3 from the current git-hub and get the foll...

Has anyone been successful in getting CUDA to work on an OSX 10.11 system? I have tried the precompiled OpenMM 6.3 and OpenMM compiled from the github, but neither seems to recognize CUDA, though it does run using OpenCL. I was using the latest CUDA toolkit and drivers but tried CUDA 7.0/6.5 with th...

Dear Peter, Following up on my post in the other forum: The reason I compiled this was to be able to take advantage of Peter's bug fix to the issue with the CustomCompoundBondForce, however, as demonstrated with the attached tar file providing a simple test that if I either of the two CustomCoumpoun...

Dear Michael and Peter, Unfortunately, even though the option to increase the identifier length exists, it cannot go beyond 62: Fatal Error: Maximum supported identifier length is 63 Thus, this isn't a solution. I have simply commented out those two functions in the fortran wrapper as a temporary fi...

Dear Peter, I pulled the github repository to build from this for testing/development of the OpenMM/CHARMM interface and find that (differing from the 6.2 release code) that there are two function names that exceed the maximum allowed in length of a function/subroutine name in fortran2003 of 63 char...

Dear Peter, Happy New Year. I discovered independently that I could add a "small" parameter to the sqrt and get this to work. Thanks for following through. However, I continue to be plagues using this functionality. I am attaching a gzipped tar file containing a couple of tests fail1.py and fail2.py...

Dear Peter, I have been playing further with the problem I raised a day or so ago, and I am convinced there is an issue in the function interpreter. I append a simple model, 1 particle, only customcompoundbonded force defined, pdb coordinates and a simple python script that runs this. If you have in...

Something is still odd, because when I replace the expression with: <Force energy="mult*step(dlta)*0.5*frc*dlta*dlta;dlta=r-droff;r=sqrt(r2);mult=step(abs(r2)-small);r2=delax*delax+delay*delay+delaz*delaz;delaz=delz-r1*zdir;delay=dely-r1*ydir;delax=delx-r1*xdir;r1=delx*xdir+dely*ydir+delz*zdir;delz=...

Dear Colleagues, I am using CustomCompoundBondedForce to generate some custom restraints associated with restraining particles, or the center of mass of a collection of particles, within a sphere, cylinder or a plane. I am running into a problem for cases where a particle (or the COM of a collection...