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## Re: [ESPResSo-devel] harmonic potential

 From: harmanda Subject: Re: [ESPResSo-devel] harmonic potential Date: Fri, 24 Oct 2008 10:18:56 +0200 User-agent: Internet Messaging Program (IMP) H3 (4.1.4)

```Hi All,

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Just a small contribution this interesting discussion about harmonic potentials.
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A) First of all harmonic potentials are used in the atomistic modeling to mimic the real chemical bonds. They are good approximation for such cases as long as we don't model extreme cases where chemical bonds can break (very rare if we consider that a chemical bond has a strength of about 1-2 EV). For such extreme cases these potentials are wrong.
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B) Concerning the CG models, the case is different because such harmonic potentials are much softer than the atomistic ones. As Burkhard said, harmonic potentials are good only for model cases like a comparison with a Gaussian chain. But if we simulate such systems under non-equilibrium conditions (eg. shear flow) then bonds can be very long, causing problems in the parallelism. As Axel explained, the length of the "bond" can become larger than the length of the box in the cell lists. But this is completely unphysical, ie. the infinite extensibility of the "bonds" is an artificial wrong result of the model. This is also the main reason why the Rouse model gives completely wrong results in the non-equilibrium dynamics of polymer melts. There is a clear solution , which we all know, to this problem (at least for most cases): the use of the FENE bonds.
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C) Now for the case that someone needs to model problems where bonds are forming and breaking during the simulation (I think there was such a problem in this list some time ago), then anyway to use harmonic potentials is not the best choice. Morse, or even Lennard-Jones, type of potentials are better.
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From the practical point of view of course a simple solution is to use a maximum distance (or better as Markus proposed a maximum energy) as the cut-off of the bond. But both solutions are purely empirical and more important they cause discontinuities in potentials and in forces. This would have a strong impact on the results.
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So I would propose to encourage people in the User Guide to not use harmonic potentials for CG simulations of problems like non-equilibrium flows or where you might have forming/breaking bonds. For the latter Morse type potentials going smoothly to zero (using for example a spline) are much more physical.
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Any more ideas-suggestions?

Best,
Vagelis

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