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:
Request by @kosovan, the initialization of globular proteins could be improved:
[ ] Currently, globular proteins are initialized at random positions, which can lead to overlaps for non-diluted solutions. We should implement a lattice-like initialization.
[x] By default, globular proteins are fixed in the simulation box and the user has to enable its motion using a built-in function in pyMBE. It would be more intuitive to do it the other way around, which is also the standard in Espresso
@kosovan @paobtorres UPDATE on this topic after revisiting the features for globular proteins:
I think that the current workflow of having a fixed globular protein as "default" and then forcing the user to enable its motion if needed is actually the way to go. Enabling the motion of the protein as a rigid objects requires additional setups (defining virtual sites, adding proper mass and moment of inertia to the central particule) that the fixed object does not.
We still should work in better initialization strategies if we want to enable simulations with several globular proteins
Request by @kosovan, the initialization of globular proteins could be improved: