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Re: [ESPResSo] Creation of Rigid Structures in Espresso

From: Mehmet Sayar
Subject: Re: [ESPResSo] Creation of Rigid Structures in Espresso
Date: Mon, 02 Feb 2009 14:21:08 +0200
User-agent: Thunderbird (X11/20081227)

Dear Lorenzo,

I have used bond angle harmonic potential to mimic a stiff polymer chain.
The details of the simulation can be found
M. Sayar & C. Holm Euro. Phys. Letters 77, (2007) 16001.

Briefly: I had polyelectrolyte chains of 30 beads each. The beads were connected
via Fene bonds. The harmonic angle potential had a stiffness parameter of 100
kT. I as able to simulated such a system with a time step of 0.005.

This of course, gives you only semi-flexible chains. In my case, the persistence
length of the chains were orders of magnitude longer than the 30 bead chain,
which was sufficient for me. Note also that, since my beads were also charged,
there was also some electrostatic contribution to the persistence length.

Let me know if you need any further info.

All the best,


Lorenzo Isella wrote:
> Dear All,
> My problem is that I would like to create e.g. a linear chain
> consisting of 8 particles. Each particle is connected e.g. to its left
> neighbor via a single contact point.
> Ideally, this chain should be a perfectly rigid body. What is the best
> way to create such a thing in Espresso? Should I use bond-angle
> interactions as described in the user guide or is there any better way
> for doing this?
> Many thanks
> Lorenzo
> _______________________________________________
> ESPResSo mailing list
> address@hidden

Mehmet Sayar - Assist. Prof.  Koc University
Email:address@hidden        Dept. Mechanical Eng.
Phone:+90-212-338-1840        Rumelifeneri Yolu, Sariyer
Fax:  +90-212-338-1548        34450 Istanbul, Turkey

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