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On a clean build of OpenMM 8.1.1 I get the following failed tests:
```txt
~/openmm-8.1.1/build$ ctest --rerun-failed --output-on-failure
Test project /path/to/openmm-8.1.1/build
Start 15: Te…
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After preparing my files in gromacs(please let me know if there is any other way of doing this) I tried :
python openbpmd.py -s solv_ions.gro -p topol.top -o ligand0_pose0 -lig_resname MOL -nreps 5
…
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**Expectation**
1. Positions obtained from an interchange object should include all the particles in the system, including virtual sites.
2. Various API points for getting positions should all lea…
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It would be great to have live visualization (preferably VMD) through this application. See feature described in Section 3.4.7 of the OpenMM Zephyr 2.0 User Guide.
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Add Jupyter Notebook examples on US simulations of particle in a model potential (in OpenMM), for:
- [x] 1D US
- [x] 1D to phi-ensemble reweighting
- [x] 1D to 2D reweighting
- [ ] 2D US
- [ ] …
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Hi,
I am new in OpenMM Simulation, but I would like to run a simulation for representatives from PDBBind dataset.
I encountered a problem with the first complex I chose - 6G84.
I ran DockPrep usi…
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My question is whether the energy computed using the NonbondedForce should differ when using 1) LJPME or 2) PME with dispersion corrections included.
When computing the energy for a single frame us…
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Hi, I found two problems when performing molecular dynamics simulations using MACE-OPENMM.
1. Multiple GPU cards can be applied without error. But there is only one GPU card running the operation.
2…
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It would be great if we could add one or two of the CB7 host-guest systems from SAMPL that @bas-rustenburg and @pgrinaway are working on, since I think this would be a nice, simple system to study bim…
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We have recently acquired an H100 system with NVlink, which requires a CUDA version of 11.8 or above, but CUDA 12 is recommended for the best performance. I've read here that CUDA 12 is not binary co…