[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: Excluding intra-molecular electrostatic interactions

From: Margaret Rosenberg
Subject: Re: Excluding intra-molecular electrostatic interactions
Date: Fri, 18 Sep 2020 14:23:36 +0200
User-agent: Roundcube Webmail/1.4.8

Hi Rudolf,

I tried the check and in my case (virtual sites only touching) the total forces and torques are negligible. Thanks for the advice!

Am 17.09.2020 18:09, schrieb Rudolf Weeber:
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:
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

Margaret Rosenberg, MSc

Dipolar Soft Matter Group
Faculty of Physics, University of Vienna
Sensengasse 8/18, 1090, Vienna, Austria

Phone: +43-(0)1-4277-73270

reply via email to

[Prev in Thread] Current Thread [Next in Thread]