Search found 7 matches

by David Minh
Sat Oct 01, 2016 9:28 pm
Forum: Molmodel: SimTK molecular modeling API
Topic: Molmodel trunk updated to use Simbody 3.0
Replies: 3
Views: 1292

Re: Molmodel trunk updated to use Simbody 3.0

Does Molmodel work with the latest Simbody, 3.5.4? I'm not sure how to set all the options for Simbody_*.
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Screen Shot 2016-10-01 at 11.26.55 PM.png (198.53 KiB) Viewed 969 times
by David Minh
Fri Nov 01, 2013 3:51 am
Forum: OpenMM
Topic: OS X Mavericks?
Replies: 19
Views: 3051

Re: OS X Mavericks?

On another machine without CUDA: pauling14:examples admin$ python testInstallation.py Failed to import OpenMM packages: dlopen(/Library/Python/2.7/site-packages/simtk/openmm/_openmm.so, 2): Symbol not found: __ZN6OpenMM13CustomGBForce11addFunctionERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9a...
by David Minh
Fri Nov 01, 2013 3:46 am
Forum: OpenMM
Topic: OS X Mavericks?
Replies: 19
Views: 3051

Re: OS X Mavericks?

I used the precompiled libraries. Maybe I can try a recompile.
by David Minh
Thu Oct 31, 2013 2:05 pm
Forum: OpenMM
Topic: OS X Mavericks?
Replies: 19
Views: 3051

OS X Mavericks?

Has anybody successfully installed and run OpenMM on a Mac using OS X Mavericks? I am using the Apple version of gcc. bash-3.2$ gcc --version Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based...
by David Minh
Tue Apr 10, 2012 6:32 am
Forum: OpenMM
Topic: Any easy way for Rigid-body MD in OpenMM?
Replies: 8
Views: 1530

Re: Any easy way for Rigid-body MD in OpenMM?

Good, I'll give it a shot.
by David Minh
Wed Apr 04, 2012 7:47 pm
Forum: OpenMM
Topic: Any easy way for Rigid-body MD in OpenMM?
Replies: 8
Views: 1530

Re: Any easy way for Rigid-body MD in OpenMM?

Yes, that would be great!
by David Minh
Wed Apr 04, 2012 1:55 pm
Forum: OpenMM
Topic: Any easy way for Rigid-body MD in OpenMM?
Replies: 8
Views: 1530

Re: Any easy way for Rigid-body MD in OpenMM?

I have a related question. I would like to do a docking-like calculation with a rigid receptor and flexible ligand, so that the ligand is sampled from the Boltzmann distribution for a given receptor conformation. So it isn't quite a rigid-body MD. Would OpenMM be able to do this type of calculation?