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 ...

See:

https://github.com/Gallicchio-Lab/openm ... ils.py#L78

as an example. It uses CustomCentroidBondForce.

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...

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...

peastman wrote: ↑

Thu May 13, 2021 9:00 am

If there's a CustomCentroidBondForce (or any other bonded force) connecting them, it will consider them to be a single molecule and always wrap them as a unit.

Great. It makes sense. Thanks!

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...

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

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...

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 ...

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...