Dear Peter, dear community, I'm thinking of porting an enhanced sampling scheme, that has been successfully demonstrated for protein-peptide binding [1], to OpenMM. I would like to ask for advice. The enhanced sampling scheme can be best described a "Replica exchange between differently boosted Lenn...

Dear all, OpenMM's NonbondedForce class offers the possibility to set an exception that overrides the normal force field parametrization for the Coulomb and Lennard-Jones interaction between two given particles. I plan to do a Hamiltonian replica exchange simulation and I thought about using this fe...

Thanks for the swift reply. Setting the atom positions again in the second example solved the problem. Concerning the first problem. How do I get the patch, once it's fixed? Will it be published on simtk? Meanwhile I was able to find a workaround for the problem. The program will not crash if the mi...

Dear Peter, I found something that looks like a bug in OpenMM 5.0. This was produced on intel 64 bit systems with gcc 4.6.3 or 4.3.4 using either a GeForce GTX 580 or a Tesla S2050 GPU and the CUDA platform. In the first example, I get a segmentation fault when I try to minimize the energy after cre...

Hi Jonathan, From my experimentation with OpenMM 5.0 I found that there are several things that can go wrong here. Have you cheked that * cicc (executable part of CUDA) is in the executable PATH? * CUDA headers are in the include path (CPATH)? It might be useful to look at the error strings that are...

Hi folks, I just tried out the new 5.0 version of OpenMM. I used the binary 64bit package for Linux. However, the testInstallation.py script failed with the message | Error launching CUDA compiler: 32512 | sh: /usr/local/cuda/bin/nvcc: No such file or directory Now it turned out that my CUDA install...