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What do you think about adding a page to make it easy to cite OpenMM, like [MDTraj does](http://mdtraj.org/1.9.3/)?
![image](https://user-images.githubusercontent.com/3656088/64926726-e2cf9300-d7ce-1…
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For now I am going to drop OSX from the testing matrix, `openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb` & `showcase/openfe_showcase.ipynb` times out
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I have a simulation trajectory file from openmm in dcd format, but it does not contain any unitcell information. Is there a way to update the unitcell information in the dcd file and save it with unit…
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Hi,
I was trying to add a global parameter to my torchForce, but I could not figure out how to make it work along with the PBC. Could you help me have a look?
Here is the structure of my torchF…
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Just making a note that we should backport https://github.com/openmm/openmm/pull/2829
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Hello,
I am trying to run a Metadynamics Metainference simulation with multi replicas using OpenMM and Plumed. I am using the [OpenMM-Plumed](https://github.com/openmm/openmm-plumed) plugin to add …
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I am planning to write a new force that uses the RMSD between molecules and I will use the OpenMM RMSDForce as a base.
The first thing I did was to include in the plugin the OpenMM RMSDForce, which I…
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When running the openmm engine with ```{'OpenCLDeviceIndex' : '1'}``` set, it always runs on device ```0``` instead of the given `DeviceIndex`. This is the full engine generating script.
```python
f…
sroet updated
7 years ago
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I am trying to create a Virtual Site (VS) in Sire with parameters that are stored in a "virtual-sites" property of a molecule. I am testing my implementation by running single point energy calculation…
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Hello,
I was following the "Pratope-epitope Docking using AbDock" pipeline inside the AbDock folder. When executing the script optimize_ab.py, the following error came up:
$ python optimize_ab.py…