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Probably just me having issues with peptide.py #92
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I suspect that the actual issue is with the format of your observable file. It seems that it has been read improperly and the error has propagated up to this function. The |
import numpy as np
import pandas as pd
S = []
df = pd.DataFrame(np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]]), columns = ['a', 'b', 'c'])
S.append(df["b"])
S Than S is a list. I tried to extract |
You are actually both right. The error raises because
|
Trying to get the peptide script running see [issue](pyMBE-dev#92)
Hello, I've been trying what @pm-blanco suggested and took inspiration from In the ValueError:
get_dt: Row 2 dt = 1.0000000000047748 = 173.000000000462 - 172.00000000045722 not equal to dt_init = 0.0 Printing the time (from |
@Zitzeronion thank you for reporting this and for the typo fix in your PR. The issue actually comes from another deprecated logic in how to run the simulation presented in for step in range(Samples_per_pH+steps_eq):
if np.random.random() > probability_reaction:
espresso_system.integrator.run(steps=MD_steps_per_sample)
else:
cpH.reaction( reaction_steps = total_ionisible_groups) in here in one simulation step one either does MC moves or MD moves. We decided to remove this logic in our current scripts because when estimating the autocorrelation times of the observables sampled the sampling time became ambiguous. Instead, now we run both MC and MD in every simulation step: for step in range(Samples_per_pH+steps_eq):
espresso_system.integrator.run(steps=MD_steps_per_sample)
cpH.reaction( reaction_steps = total_ionisible_groups) we want to enforce this logic when using our analysis framework, that is why |
Trying to get the peptide script running see [issue](#92)
The peptide.py script produces an error for me:
As far as I understand
Z_pH
does not have time intervals saved. I tried to find a fix using the tests folder but wasn't yet able to do so. I am using espresso v4.2 and pyMBE v0.8.The text was updated successfully, but these errors were encountered: