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Hello,
I am interested in molecular dynamic simulations for systems other than proteins/membranes, etc.
Specifically, I want to run simulations for system like carbon nanostructures or boron-ni…
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Compilation and "make PythonInstall" now works.
However when I try to issue "from openmmnn import *" in python I get:
```
>>> from openmmnn import *
Traceback (most recent call last):
File ""…
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I am really excited about the Drude support in ParmEd.
When I was trying to convert an OpenMM Topology to a ParmEd Structure and save it afterwards, an AttributeError occurred.
`omm_psf = openmm.ap…
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Hi,
_For reference, I am running the latest version of parmed v3.4.3_
I have a GROMACS .top file for a protein-ligand system using the Amber 99sb-idln forcefield (NB I was not the one to paramet…
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I want to run torsion scans with Parsley and OpenMM on the OpenFF Substituted Phenyl Set 1. The JSON for the inputs are here:
https://github.com/openforcefield/qca-dataset-submission/blob/master/20…
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I'm wondering if it would be feasible to allow `parmed.openmm.load_topology(topology)` to identify angles as well--currently it seems to only do that if there is a `System` as well. I realize the pres…
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## Expected Behavior
Attempting to predict the structure of a homodimer using colab with stock settings, plus amber relaxation of only the top-ranked final structure.
## Current Behavior
After fi…
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Hi everyone,
I am trying to use the MDTraj XTCReporter with OpenMM to write to a .xtc file. I have successfully used it to run a 500 us trajectory with positions saved every 20 fs (yes, a lot, but…
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Observing the following in logs in `dev` environment:
```
Exception occurred extracting snapshot from /home/server/server2/projects/13456 data /home/server/server2/data/SVR916310614/PROJ13456 run …
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I learned that Openmm can apply force to calculate viscosity by non-equilibrium method, but I need to run the trajectory file again, is there a way to output pressure tensor to calculate viscosity b…