bump
I am currently building a CG simulation of a white blood cell. I currently have constituent particles interacting according to either a specialized angular-dependent potential (for the lipid bilayer), or standard lennard-jones potentials. To represent the cell cytoskeleton I would like to apply soft glassy rheology theory (SGR), but have been struggling to find a potential in LAMMPS for this. The principle of the theory is that particles exist within a energy landscape of potential wells of varying depth, with particles then able to “hop” between these wells according to a probability function, dependent on their energy. This then describes a glass-like flowing material. This theory was developed by Sollich et al. 1997 (Sollich P., Lequeux F. et al.: Rheology of soft glassy materials, Physical Review Letters, Vol. 78, (1997), pp. 2020–2023)
Do you know of any potentials that already exist in LAMMPS to apply SGR, or could be repurposed to it?
Thanks,
Paul
If this can be reduced to a complicated pair potential, have you considered pair_style table?
I am currently building a CG simulation of a white blood cell. I currently have constituent particles interacting according to either a specialized angular-dependent potential (for the lipid bilayer), or standard lennard-jones potentials. To represent the cell cytoskeleton I would like to apply soft glassy rheology theory (SGR), but have been struggling to find a potential in LAMMPS for this. The principle of the theory is that particles exist within a energy landscape of potential wells of varying depth, with particles then able to “hop” between these wells according to a probability function, dependent on their energy. This then describes a glass-like flowing material. This theory was developed by Sollich et al. 1997 (Sollich P., Lequeux F. et al.: Rheology of soft glassy materials, Physical Review Letters, Vol. 78, (1997), pp. 2020–2023)
Do you know of any potentials that already exist in LAMMPS to apply SGR, or could be repurposed to it?
I am not aware of a potential in the LAMMPS distribution that fits your description out of the box. However, I don’t have the time to read up on the model to know whether the “hopping” is part of the potential function or implemented otherwise. Please note that since LAMMPS can be easily customized, there may be a model you are looking for out there, just not submitted for inclusion into the the LAMMPS distribution. The way to find it would be to search the published literature (you definitely should prefer an implementation that has seen peer review unless you are willing to do thorough testing and possible bugfixing yourself) or the web. There are over a thousand forks of the LAMMPS github repo alone (although there are probably not so many people doing research in the specific field of research you are interested in), so there is a finite probability that one of them has something useful.
and there may be more changes that are just uploaded to websites as files or as a source repository not forked from LAMMPS itself.
axel.