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Here is the definition of the global interpreter lock (GIL) in the Cython documentation ([link](https://cython.readthedocs.io/en/latest/src/userguide/glossary.html#term-Global-Interpreter-Lock-or-GIL)…
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I am getting an error at the example 6 (steepest descent) step:
```
steepest_descent = ProtoSyn.Drivers.SteepestDescent(energy_function, callback, 500, 0.001, 0.1)
steepest_descent(pose)
```
I…
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Hi all,
I've been looking at speeding up my FEP calculations. While I've been looking at increased end state sampling using a variety of enhanced sampling methods, an easy win looks like using hydr…
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### 🐛 Describe the bug
```python
import torch
import functorch
import jax.numpy as jnp
import jax
x = torch.tensor(0.5 + 0.5j, dtype=torch.complex128)
def fn(x):
return x.sin()
jacf…
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The slide says
> Neg. risk gradient points in the direction of **the steepest descent**
This is only true if we use the $L_2$ norm
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cc @alanlujan91
This article outlines `Bayesian Optimization`, a method of computing $x$ that optimizes $f(x)$ when $f(x)$ is hard to sample and non-differentiable.
https://towardsdatascience.c…
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Hi, I have a question about filter optimization for DiMP.
I know DiMP uses steepest descent for filter optimization. I found the implementation of steepest descent in here [ltr/models/meta/steepest…
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Looking at the [Example 4](https://github.com/sergio-santos-group/ProtoSyn.jl/blob/dev/examples/4-energy-calculation.ipynb), I came across an error when calculating forces. It is thrown when running `…
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I'm trying to run a simulation using gromacs topology and coordinate files. When I try to load the topology file I get the following error:
.....
File "gromacstopfile.py", line 247, in _process…
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The following script shows the bug:
``` python
import sys
import numpy as np
import espressomd
system = espressomd.System(box_l=[10.0] * 3)
system.virtual_sites = espressomd.virtual_site…