Search found 13 matches
- Mon Jul 15, 2024 3:05 pm
- Forum: OpenMM
- Topic: Is it possible to run FEP with NNP?
- Replies: 3
- Views: 388
Re: Is it possible to run FEP with NNP?
This was done with a modified version of AToM-OpenMM: Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials https://pubs.acs.org/doi/abs/10.1021/acs.jcim.3c02031 If interested, I recommend contacting the corresponding authors, Francesc Sabanes Zariquiey and Gianni De ...
- Tue Nov 29, 2022 10:11 am
- Forum: OpenMM
- Topic: adding distance constrain between the centers of two molecules
- Replies: 2
- Views: 164
Re: adding distance constrain between the centers of two molecules
See:
https://github.com/Gallicchio-Lab/openm ... ils.py#L78
as an example. It uses CustomCentroidBondForce.
https://github.com/Gallicchio-Lab/openm ... ils.py#L78
as an example. It uses CustomCentroidBondForce.
- Thu Aug 18, 2022 9:48 am
- Forum: OpenMM
- Topic: FES convergence issue on metadynamics simulation
- Replies: 2
- Views: 222
Re: FES convergence issue on metadynamics simulation
One way to test convergence is to monitor the number of independent visits to a set of chosen conformational states. If a state is visited only once during the simulation, its free energy is unlikely to be converged. Testing convergence of free energy landscapes for bounded regions of conformational...
- Tue Nov 16, 2021 8:14 am
- Forum: OpenMM
- Topic: Install OpenMM without Conda
- Replies: 5
- Views: 215
Re: Install OpenMM without Conda
To install the OpenMM libraries without Conda we like to have: set(PYTHON_SETUP_COMMAND "install --prefix=${CMAKE_INSTALL_PREFIX}") in wrappers/python/CMakeLists.txt instead of the default, which I think is set(PYTHON_SETUP_COMMAND "install --root=\$ENV{DESTDIR}/") That way the python wrappers are i...
- Thu May 13, 2021 9:44 am
- Forum: OpenMM
- Topic: Does OpenMM automatically image the molecule's positions?
- Replies: 9
- Views: 236
- Thu May 13, 2021 5:49 am
- Forum: OpenMM
- Topic: Does OpenMM automatically image the molecule's positions?
- Replies: 9
- Views: 236
Re: Does OpenMM automatically image the molecule's positions?
That's just how the code is written. It might be possible to restructure the algorithm in a way that wouldn't require it. We have restraint potentials implemented using CustomCentroidBondForce to keep two molecules near a certain vector displacement (offx, offy, offz) based on for example: d12 = sq...
- Tue May 11, 2021 1:00 pm
- Forum: OpenMM
- Topic: Does OpenMM automatically image the molecule's positions?
- Replies: 9
- Views: 236
Re: Does OpenMM automatically image the molecule's positions?
Can you explain why the barostat algorithm requires the wrapping? In principle, the shape and volume of the box are inputs of the potential energy function, not a property of the configuration of the molecules.
Thanks
Emilio
Thanks
Emilio
- Fri Apr 03, 2020 12:03 pm
- Forum: OpenMM
- Topic: OpenMM/SDM Build Docker Box
- Replies: 1
- Views: 106
OpenMM/SDM Build Docker Box
So we are locked out of our offices in Brooklyn College, the network went down and we lost access to our CentOS build machine. We set out to replace it with a virtual machine to use at home. It seems that the core OpenMM's developer community uses a docker image for this purpose, but we have not bee...
- Thu May 30, 2019 3:50 pm
- Forum: OpenMM
- Topic: Malloc error
- Replies: 9
- Views: 428
Re: Malloc error
I have been getting malloc() errors due to singularities in the forces. See for example https://github.com/pandegroup/openmm/issues/2244
The fact that the crashes are dependent on atomic configurations suggests that the same thing might be happening here ...
The fact that the crashes are dependent on atomic configurations suggests that the same thing might be happening here ...
- Wed Oct 24, 2018 5:43 am
- Forum: OpenMM
- Topic: Desmond cms file
- Replies: 8
- Views: 265
Re: Desmond cms file
If the problem is just in the OpenMM DMS importer, let's fix that. Other combining rules aren't a problem. We already do that for CHARMM, for example. I will submit a pull request to add OPLS capability to DesmondDMSFile. However, the larger issue I think is that there is a lack of tools to prepare...