Yutong Zhao
Yutong Zhao
I'm looking for a method that lets me specify a list of distances to minimize the RMSD against. i.e. Given two point clouds each with size N, and a 1-1...
I'm looking to implement custom GPU ops similar to how tensorflow allows for defining custom jvps. Is there a similar tutorial/guide on how feasible this will be with jax?
``` python import jax import jax.numpy as np import numpy as onp def E_fn(conf): ri = np.expand_dims(conf, 0) rj = np.expand_dims(conf, 1) dxdydz = np.power(ri - rj, 2) dij =...
In alchemical free energy calculations, we often need to define torsions and angles in a way that may introduce numerical instabilities (eg. morphing into nitriles, ring opening/closing, etc.). Typical symptoms...
For certain types of overlapping distributions, the uncertainty estimate returned by BAR can be`nan` ``` python %matplotlib inline import numpy as np import pymbar from matplotlib import pyplot as plt...
We should assert that for rectangular boxes, the diagonal elements are zero, as a box size of zero is just undefined behavior. jfass pointed out that it probably suffices to...
We currently enforce ring completion in the MCS protocol, we should probably switch to: ``` def mcs_map_simple(a, b, threshold: float = 0.5, timeout: int = 5, smarts: Optional[str] = None):...
Introduction of chiral restraints implies that we should probably (on the first pass) check and flag when a chiral inversion is explicitly defined.
Our current harmonic angle oscillator has an option for `cos_angles` that we default to `True`. The original motivation for this was to avoid the numerical singularity that arises at 0...