Dear All,
Thanks for the suggestions. I just have some quick questions. I understand the main idea that was suggested by Steve and Axel but I have a few questions. If I want to place a rigid body at the ends of the ellipsoids. Should I use the body atom style in conjunction with ellipsoid atom style. if this is the case then I wont be able to connect them with bonds because i need to include the molecular atom style. My question is simply what atom style should I use in conjunction with ellipsoid so that I can create that rigid particle at the end of the ellipsoid. Also How to pin that particle to the ellipsoid. My final question how would I ensure that I connect the ends of the rigid particles only with out include the center of mass of the ellipsoid. I have attached a schematic for simplicity sorry if it is not that perfect.
Regards,
Elena
Dear All,
Thanks for the suggestions. I just have some quick questions. I understand
the main idea that was suggested by Steve and Axel but I have a few
questions. If I want to place a rigid body at the ends of the ellipsoids.
Should I use the body atom style in conjunction with ellipsoid atom style.
no.
if this is the case then I wont be able to connect them with bonds because
i need to include the molecular atom style.
you can combine atom styles via the hybrid atom style. so, the tethering
points can be (practically massless) point particles with bonds
My question is simply what atom style should I use in conjunction with
ellipsoid so that I can create that rigid particle at the end of the
ellipsoid. Also How to pin that particle to the ellipsoid.
use fix rigid to combine two point particles with one ellipsoid particle
into one rigid object.
My final question how would I ensure that I connect the ends of the rigid
particles only with out include the center of mass of the ellipsoid. I have
attached a schematic for simplicity sorry if it is not that perfect.
you only form bonds between the point particles, i.e. tether points.
axel.
to satisfy my own curiosity, i made a (very crude) attempt to build such a tethered ellipsoid system. i am certain, that this is not 100% correct (e.g. the potential parameters are completely made up (POOMA!), and to correctly compute temperature for such a system is a bit complex, since only the aspherical particles should be counted, but those have 3 additional degrees of freedom which require a special temperature compute, yet fix rigid will subtract degrees of freedom including those for the point particles… i also didn’t check the orientation of the ellipsoids), but hopefully sufficient to show the principles and provide you with a reference that at least runs and produces a trajectory that doesn’t look completely wrong.
as i already mentioned, this is going to be complicated and will require careful testing and detailed reading of the documentation and related papers.
it is going to be much easier and safer to build those rigid objects from multiple lennard-jones point particles (BTW: i started creating this input deck by building such a system and then adapted it by replacing atom and pair styles and converting the center particles of each 3-atom group to an ellipsoid). so if your intended model can be approximated by that, you’ll save yourself a massive amount of trouble and headache.
axel.
in-connected-ellipsoids (696 Bytes)
connected-ellipsoids.data (891 Bytes)
Thanks Axel,
I really Appreciate your help.
Regards,
Elena