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I am trying to use ParmEd v3.4.3 to convert a system solvated in tip4pew water from openMM v. 7.7.0 to GROMACS topology and configuration files (gro). Python lines doing the conversion are reported be…
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We'll need to create `OEMol` objects from components of an OpenMM `Topology` as discussed in #18 . Assuming these topologies contain connectivity, element, bond order, and formal charge, this should b…
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I just encountered the error written in the title.
`InvalidSpec: The package "nvidia/linux-64::cuda-compiler==12.5.0=0" is not available for the specified platform`
I have installed AF in several c…
ocstx updated
1 month ago
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My issue is related to the truncated octahedron box conversion to triclinic, which has been discussed before. However, there are some issues that I think might be worth addressing for OpenMM. For back…
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Hi
I created a branch vsites2 and uploaded the changes contained in one commit here:
https://github.com/bieniekmateusz/Sire/tree/vsites2
There are some useful code snippets I left in the code t…
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After compiling plumed, openmm, and openmm-plumed locally, I would have thought that the force script utilizes plumed native parsing. However, I cannot reference the additional plumed modules through …
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Do we need an `__init__.py` to simplify test system import?
Currently, it seems we'd need to do something like
``` python
from testsystems.test_systems import HarmonicOscillator
```
Instead, we'd l…
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Is it possible to employ the APPLE&P force field within OpenMM? I possess the requisite parameters and seek to conduct simulations using these parameters within OpenMM. Especially, I am interested in …
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AmberTools23 includes a new GAFF version (2.2.20, March 2021). From the header:
```
AMBER General Force Field for organic molecules (Version 2.2.20, March 2021)
```
We should add this GAFF version…
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Does openmm-torch support multivariate collective variables? I would like to do metadynamics along an NN collective variable in 3 dimensions, and the current openmm-torch documentation involves only u…