and.tos

I did not make any changes to the code, but want to use it to run on a private dataset. For this I defined the following configuration: ``` PotentialNet_inhouse =...

The code works if I set: distance_bins': [1.5, 2.5, 3.5] I suggest that ``` def int_2_one_hot(a): """Convert integer encodings on a vector to a matrix of one-hot encoding""" n =...

Hi Lukas, thanks for your response. My matrix is actually larger. I am trying to get this to run and provide feedback.

I am now running into a zero division error: print(len(c_l)) gives me 46, which is the number of simulation windows print(c_l[0].shape) gives me (10, 10). 10 is the number of...

I am using Amber, so the unit of the force constant should be kcal/(mol*A²) and thus that of the potential kcal/mol.

Hi Lukas, the error appears when I try to calculate the uncertainty. Here's a test case: ```python import numpy as np import matplotlib.pyplot as plt from pydhamed import count_matrix from...

Hey, I think the error comes from some frames lying outside of the most left and most right bin. I fixed this by changing the bin distribution. Now I get...

Thanks for your feedback! I ran an umbrella sampling to calculate the free energy of binding for a ligand to a protein. You're right, executing run_dhamed within the loop is...

I am currently running it on the full data set. I'll let you know once it's finished.

Hi Lukas I am still getting the division by zero error on the full data set. Should I send you the complete input?