[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: Excluding intra-molecular electrostatic interactions
From: |
Rudolf Weeber |
Subject: |
Re: Excluding intra-molecular electrostatic interactions |
Date: |
Thu, 17 Sep 2020 18:09:43 +0200 |
User-agent: |
Mutt/1.9.4 (2018-02-28) |
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