Hi Margaret,
On Thu, Sep 17, 2020 at 05:06:32PM +0200, Margaret Rosenberg wrote:
I'm attempting to use pypresso to simulate a system of anisotropic
charged
colloids. Each of these colloids is represented using the raspberry
model.
Following the documentation, I've excluded steric interactions between
virtual sites on the same molecule. However, I also need to add a
charge to
each virtual particle: how can I exclude Coulomb interactions between
virtual sites in the same colloid?
There is this bonded interaction:
http://espressomd.org/html/doc/espressomd.html#espressomd.interactions.BondedCoulombSRBond
and also a variant for pure 1/r.
Depending on what you intend to do, excluding the electrostatic ia
between the particles making up a rigid body may not be necessary.
In theory, pair-wise interactions within the virtual sites of a rigid
body add up to zero due to Newton's thhird law.
For steep potentials like Lennard-Jones, some of the contributions to
the sum might be huge though, if your virtual sites are "overlapping"
based on the Lennard-Jones sigma.
So due to numerical errors, the total force might end up being
non-zero.
For 1/r, it might well be less of an issue.
To check, integrate a single free raspberry for a few time steps and
check that the force and torque on the central, non-virtual particle
remain zero.
I mostly just use a specific particle type for the beads in a
raspberry and only define interactions with respect to other particle
types. I.e., there is no LJ interaction within the raspberry in the
first place.
Regards, Rudolf