|Subject:||[ESPResSo-users] Creating polymers: Default neutral monomer type not 0?|
|Date:||Wed, 21 Feb 2018 17:06:43 +0100|
Dear ESPResSo users and developers,
I am trying to simulate and visualize polymers in confinement. I'm working on the basis of the minimal-polymer.py sample file in the current development version. This file (and some other sample files) define i.a.:
A) a shifted and truncated Lennard-Jones potential between all monomers, defined by system.non_bonded_inter[0, 0].lennard_jones.set_params(...)
B) one or more polymers created by polymer.create_polymer(...)
At B), no type_poly_neutral or type_poly_charged is given. Given the documentation [ http://espressomd.org/html/doc/espressomd.html#espressomd.polymer.create_polymer ], one expects that the monomers will be of type 0 by default, as they are not charged. Instead, a simple printout of the created particles shows that they are of type 1. To change the type to int n, an explicit argument to create_polymer of the form type_poly_charged=n works. Note that type_poly_neutral=n does *not* work, even though the monomers are in fact neutral. Thus, it seems as if create_polymer somehow confuses the charge/neutrality of the monomers it intends to create.
If one changes minimal-polymer.py by setting the particle type to 0, or the interaction to non_bonded_inter[1, 1], the L-J-potential is indeed working on the polymer's monomers. As far as I can tell, it *not* working in the current version.
However, once it is activated, many 'bond broken' errors arise. I'm not entirely sure about the cause, but these errors are probably to be expected, as a proper activation of such potential should start with a force-capped warm-up phase. This might be necessary to add to this (and some other?) sample files.
As I am just starting with ESPResSo this month, I am still not quite sure about its proper usage, so... I would appreciate any insights into whether this is a bug, or that I am mistaken.
Many thanks in advance,
and best regards,
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