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If the Nose-Hoover dynamics is chosen in ASE (ase.md.npt.NPT), there is an error with the calculated bias forces:
File "/pysages/backends/ase.py", line 105, in wrapped_step
simulation._step(forc…
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Hi PySAGES developers, first thank you again for the nice code!
I've seen some codes regarding JAX-MD as backend simulator, but have not yet figured out how I could use it for metadynamics. Does PyS…
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Writing the results in a .dat file is one way of doing this.
I think the more python way of doing it, would be to pickle the results.
But either is fine.
_Originally posted by @InnocentBug in htt…
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As mentioned here https://groups.google.com/g/ipi-users/c/JlWokLv0oe8, the https://github.com/SSAGESLabs/PySAGES development team is interested in interfacing with i-pi. For this, we would need to wor…
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Code:
```
import jax
import jax.numpy as jnp
import numpy as np
import sys
import hoomd
import hoomd.md
from ecv.models import AutoEncoder
from ecv.models.encoders import MLP, EGNN
fr…
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I am not sure if this is a known issue, but I noticed that CVs which rely on the barycenter has a small issue in OpenMM.
To my knowledge, OpenMM wraps particle coordinates internally when using PBC…
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Dear Developers,
I wonder if you can:
1. give a little guide on how to implement a per-atom collective variable. Some things are similar to [MultiColvar](https://www.plumed.org/doc-v2.7/user-doc…
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We should give the user the ability to switch free energy integration routines. We can provide this as an argument to analyze.
CC @ricalessandri
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### Additional comment:
@conda-forge-admin, please add bot automerge
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A [commit](https://github.com/beartype/plum/commit/8b43135ee0a93a8a3ffb08e75b14725b7e413562) in the plum dispatch 2.3.0 contains a change that is not well documented. The `Dispatcher.methods` [attribu…
yzjin updated
1 month ago