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Re: [ESPResSo-users] Bond Breaking in Polymer Networks - United Atom For


From: Axel Arnold
Subject: Re: [ESPResSo-users] Bond Breaking in Polymer Networks - United Atom Forcefield
Date: Tue, 13 Nov 2012 15:37:29 +0100
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:16.0) Gecko/20121026 Thunderbird/16.0.2

Hi Stefanos,

first of all, ESPResSo is not designed for atomistic simulations, therefore you need to manually setup the necessary LJ-exclusions for your model.

Regarding the bond-breaking, there is no internal mechanism yet, but broken bonds are simply reported as errors back to the scripting interface. You can catch such errors in Tcl, and remove the bond, as well as dihedrals and exclusions. In so far you can get your model to work, but your performance will depend quite on how often bonds break, since exiting to Tcl is rather slow. If a bond breaks only every 100 or so timesteps, that is probably not an issue, but bonds breaking every other time step is probably too much.

Cheers,
Axel

On 11/13/2012 11:02 AM, Stefanos Anogiannakis wrote:
Dear all,

I'm interested in performing MD simulation of polymer networks under tension,
where some chains could break as elongation proceeds.

I use a United Atom (UA) forcefield.
The bonded interactions of my model include:
(i)   a bond stretching potential
(ii)  an angle potential (bond bending)
(iii) a dihedral (torsional) potential.

The nonbonded, pairwise interactions are based on a 6-12 Lennard-Jones (LJ) potential,
which acts between all possible pairs (inter- and intra-chain),
except from intra-chain pairs that are separated by 1, 2, or 3 sequential bonds,
(the so called (1-5) intra-chain LJ potential).

I would like to ask you if ESPResSo is able to break bonds 'on the fly', as simulation proceeds,
according to a distance criterion for the bond length.

In terms of potentials, a bond scission event means that

(a) For the UAs making this bond, the bond potential will not be evaluated (or will be turned off) after breakage (b) The angle and dihedral potentials related with this bond will cease to exist (or be evaluated) (c) A LJ pairwise interaction between the UAs of the broken bond will start to apply.

Thank you very much for your help,
Stafanos.


--
JP Dr. Axel Arnold
ICP, Universit├Ąt Stuttgart
Pfaffenwaldring 27
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609




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