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Hello.
I am trying to save an espaloma parameterized system in gromacs format to run the simulations using gromacs.
I posted this issue earlier on espaloma repo https://github.com/choderalab/espalom…
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Hi Peter,
As @wardhaddadin1 mentioned yesterday in the openmm/EXS call, the neighbor list implemented in Torchani seems to assume that input coordinates are wrapped in the simulation box.
I have…
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**Description**
Thanks for a great tool, very helpful for MD simulations in OpenMM!
In my application, I often use atoms that have no parameters registerd in OpenFF (like ``openff-2.0.0.offxml``).…
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1. Add a transporter protein with direction "Efflux"
2. Add a transport process using the new transporter protein to a molecule
3. Create a simulation and send to MoBi:
sdf_files = ['bcd_gly.sdf', 'aspi…
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When I try to use "optimize" tool with following .xyz file I get a strange result:
HAc_H2O.xyz:
13 HAc_H2O
1 C 0.558027 0.163473 0.126991 209 2 3 5
2 O …
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I am trying to simulate the BCR model (https://journals.aai.org/jimmunol/article/189/2/646/86795/A-Computational-Model-for-Early-Events-in-B-Cell) using NFsim.
This is the code:
```python
import …
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Noticed while working on #136 ...
Currently, all Preferences Properties are instrumented and featured in all sims in the FEL suite. These elements should not be instrumented in sims where they are…
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I am new to CP2K and DeepMD. I have been running AIMD simulations using CP2K and subsequently parsing the data with cp2kdata. However, I encountered an issue where only 1 frame is detected in the outp…
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Hi there,
I am having issue to make system from the protein I attached. The error occurs in forcefield.createSystem with error message:
ValueError: No template found for residue 210 (LEU). The …