Search found 36 matches

by luke czapla
Wed May 14, 2014 11:52 am
Forum: OpenMM
Topic: OpenMM 6.0.1
Replies: 7
Views: 506

Re: OpenMM 6.0.1

Thanks Peter, I'm not sure because I unpack the clean OpenMM6.0.1-source.tar.gz and get that string of errors from default "cmake ." in the folder, this is on a Linux system. However, when I grab a clean "git" with the clone and type the same thing everything proceeds fine, and then I just change a ...
by luke czapla
Tue May 13, 2014 12:18 pm
Forum: OpenMM
Topic: OpenMM 6.0.1
Replies: 7
Views: 506

Re: OpenMM 6.0.1

I have installed the OpenMM distribution from libraries, but with the source I get a huge string of errors like this (I just copied a few and there's a ton associated with each folder): CMake Error at tests/CMakeLists.txt:12 (ADD_EXECUTABLE): add_executable called with incorrect number of arguments ...
by luke czapla
Mon May 12, 2014 1:11 pm
Forum: OpenMM
Topic: OpenMM 6.0.1
Replies: 7
Views: 506

Re: OpenMM 6.0.1

Thanks so much for the link and I'm updating the systems. I will let you know if I run into any problems and will proceed cautiously and validate some test runs.
by luke czapla
Mon May 12, 2014 4:22 am
Forum: OpenMM
Topic: OpenMM 6.0.1
Replies: 7
Views: 506

Re: OpenMM 6.0.1

Could you possibly elaborate on issues with PME on multiple devices and if that is a bug applicable to 6.0? I'd set up some calculations with the 6.0 routines but we didn't use them in publication-intended calculations yet and will upgrade to 6.0.1. We're really interested in using the multiple GPUs...
by luke czapla
Mon May 05, 2014 10:21 am
Forum: OpenMM
Topic: OpenCL OpenMM on Mac w/ Intel HD 4000
Replies: 2
Views: 195

Re: OpenCL OpenMM on Mac w/ Intel HD 4000

Hi Luke, At present, OpenCL is completely broken on OS X. This is caused by bugs in Apple's implementation. They're aware of the bugs. They have test cases to reproduce them. Perhaps some day they will even fix them. Unfortunately, they give us no information at all. The next update to OpenMM (due ...
by luke czapla
Fri May 02, 2014 3:17 pm
Forum: OpenMM
Topic: OpenCL OpenMM on Mac w/ Intel HD 4000
Replies: 2
Views: 195

OpenCL OpenMM on Mac w/ Intel HD 4000

Hello everyone, I have been having some trouble with certain simulations in OpenMM (utilizing CustomGBForces) using OpenCL on my MacBook Pro - it is a convenient testing platform. Here are the OpenCL parameters printed out from the context: OpenCLDeviceIndex: 1 OpenCLDeviceName: HD Graphics 4000 Ope...
by luke czapla
Tue Apr 29, 2014 12:34 pm
Forum: OpenMM
Topic: Amber GB models in C++ API
Replies: 2
Views: 199

Re: Amber GB models in C++ API

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...
by luke czapla
Wed Mar 05, 2014 12:26 pm
Forum: OpenMM
Topic: validating OpenMM energy terms
Replies: 10
Views: 618

Re: validating OpenMM energy terms

Just two brief questions. Is reassigning the Force groups in between integrator->step() calls valid? I'd like to keep them organized but then assign them to separate groups every 2000 steps or so and get their energies one by one and put them back for the next steps. How would I specify dummy partic...
by luke czapla
Tue Mar 04, 2014 1:22 pm
Forum: OpenMM
Topic: validating OpenMM energy terms
Replies: 10
Views: 618

Re: validating OpenMM energy terms

because there was OBC2 somewhere with CPU and Reference platform Oh, he's referring to GBSAOBCForce. It's uses the OBC-II parameters. And it's implemented on all platforms, not just CPU and Reference. But for CUDA and OpenCL, the speed penalty of using CustomGBForce instead of the hand-coded versio...
by luke czapla
Tue Mar 04, 2014 12:29 pm
Forum: OpenMM
Topic: validating OpenMM energy terms
Replies: 10
Views: 618

Re: validating OpenMM energy terms

I don't know what you mean by "GBOBC2Force". Perhaps you're thinking of the GBn2 model Jason added? You'll find that in customgbforces.py. Peter Thanks, he was actually saying that there was no need for customgbforces.py for this one because there was OBC2 somewhere with CPU and Reference platform ...