pyMBE provides tools to facilitate building up molecules with complex architectures in the Molecular Dynamics software ESPResSo. For an up-to-date API documention please check our website:
This becomes an issue when restarting simulations that have been set up with pyMBE since it breaks the setup of the reaction methods, which cannot be checkpointed with the current funtionalities in ESPResSo.
Here a minimal working example that shows this issue:
import pyMBE
# Create an instance of pyMBE library
pmb = pyMBE.pymbe_library(seed=42)
# Acidic particle
pmb.define_particle(
name = "A",
acidity = "basic",
pka = 4,
sigma = 1*pmb.units('reduced_length'),
epsilon = 1*pmb.units('reduced_energy'))
pmb.define_particle(
name = "C",
z = 1,
sigma = 1*pmb.units('reduced_length'),
epsilon = 1*pmb.units('reduced_energy'))
# Save the pyMBE dataframe in a CSV file
pmb.write_pmb_df(filename='df.csv')
# Here all charge numbers and espresso types are integers
print(pmb.df)
# Read the pyMBE dataframe
pmb.read_pmb_df(filename='df.csv')
# Here some of the charge numbers and espresso types are float
print(pmb.df)
# This breaks the setup of the reaction methods
pmb.setup_cpH(counter_ion="C", constant_pH=2)
@paobtorres do you want to take care of solving this?
This becomes an issue when restarting simulations that have been set up with pyMBE since it breaks the setup of the reaction methods, which cannot be checkpointed with the current funtionalities in ESPResSo.
Here a minimal working example that shows this issue:
@paobtorres do you want to take care of solving this?