Search found 53 matches
- Mon Mar 29, 2021 8:09 pm
- Forum: OpenMM
- Topic: python module "openforcefield" for small molecule residue template generators
- Replies: 5
- Views: 784
Re: python module "openforcefield" for small molecule residue template generators
Apologies for the difficulties, and thanks for reporting this! The Open Force Field Toolkit changed its namespace when it moved to conda-forge, from `openforcefield` to `openff`. We have updated the `openmmforcefields` package README with updated instructions here: https://github.com/openmm/openmmfo...
- Wed Sep 18, 2019 8:47 pm
- Forum: OpenMM
- Topic: yank , openmm and python version
- Replies: 2
- Views: 225
Re: yank , openmm and python version
Hi! Could you post this in the Yank GitHub issue tracker? https://github.com/choderalab/yank/issues
- Sun Dec 30, 2018 11:48 pm
- Forum: OpenMM
- Topic: Installing development version of OpenMM
- Replies: 4
- Views: 657
Re: Installing development version of OpenMM
The corrected dev packages are now being pushed. [chodera@lilac:chodera]$ python -m simtk.testInstallation OpenMM Version: 7.3 Git Revision: bd66a7b92df724d59be3330fd23a1450982051c5 There are 4 Platforms available: 1 Reference - Successfully computed forces 2 CPU - Successfully computed forces 3 CUD...
- Sun Dec 30, 2018 7:26 pm
- Forum: OpenMM
- Topic: Installing development version of OpenMM
- Replies: 4
- Views: 657
Re: Installing development version of OpenMM
Here's the new PR to fix: https://github.com/omnia-md/conda-dev-recipes/pull/158
I'll hopefully have this tested, merged, and new packages pushed tonight.
I'll hopefully have this tested, merged, and new packages pushed tonight.
- Sun Dec 30, 2018 7:23 pm
- Forum: OpenMM
- Topic: Installing development version of OpenMM
- Replies: 4
- Views: 657
Re: Installing development version of OpenMM
It appears the dev builds have been failing due to the development recipe not installing cython. From the travis build logs, https://api.travis-ci.org/v3/job/473543664/log.txt: OPENMM_LIB_PATH = /opt/conda/conda-bld/openmm_1546167745162/_b_env_placehold_placehold_placehold_placehold_placehold_placeh...
- Tue Mar 19, 2013 11:42 am
- Forum: OpenMM
- Topic: Planned support for Intel Xeon Phi?
- Replies: 3
- Views: 542
Planned support for Intel Xeon Phi?
Hi!
Is support for Intel Xeon Phi planned?
TACC Stampede is now operational, and features Dell PowerEdge C8220 nodes with Xeon Phi coprocessors:
http://www.tacc.utexas.edu/resources/hpc
John
Is support for Intel Xeon Phi planned?
TACC Stampede is now operational, and features Dell PowerEdge C8220 nodes with Xeon Phi coprocessors:
http://www.tacc.utexas.edu/resources/hpc
John
- Mon Feb 25, 2013 1:15 pm
- Forum: OpenMM
- Topic: Problem running openmm on Retina MBP
- Replies: 10
- Views: 1612
Re: Problem running openmm on Retina MBP
Justin,
Thanks so much for figuring this out! We were suffering from exactly this problem and couldn't make head or tail of what was going on...
Best,
John
Thanks so much for figuring this out! We were suffering from exactly this problem and couldn't make head or tail of what was going on...
Best,
John
- Thu Aug 18, 2011 3:15 pm
- Forum: OpenMM
- Topic: SanderOpenmm tests: Segmentation fault error
- Replies: 3
- Views: 426
RE: SanderOpenmm tests: Segmentation fault error
<t>Hi Vivek,<br/> <br/> Can you package up the input files you're using here?<br/> <br/> I think I've seen this error before, and in the cases I ran into, I was trying to use the wrong format for input coordinates. Is your peptide.crd file a proper restart file, with six coordinates per line, or is ...
- Mon Aug 08, 2011 10:29 pm
- Forum: OpenMM
- Topic: Release Notes
- Replies: 6
- Views: 1229
RE: Release Notes
<t>I'll second Siddharth's request to have a list of bugs fixed in each release. One of the major issues we had with gromacs was that it was difficult to figure out which bugs were fixed in which releases, which became especially problematic when we had to determine whether the new release meant we ...
- Sun Apr 10, 2011 9:47 am
- Forum: OpenMM
- Topic: Pulling a Nanowire...
- Replies: 1
- Views: 398
RE: Pulling a Nanowire...
<t>Hi Kasra,<br/> <br/> What kind of experiment is your simulation meant to mimic? Is it pulling in a laser trap? By an AFM tip?<br/> <br/> If you're simulating something like pulling in a laser trap, it might make sense to create a CustomExternalForce that traps one or more atoms at one end in a fi...