Re: [Towhee-users] Polymer chains

[Craig T. <ct...@um...>]

Jianguo,

I've attempted to perform similar simulations. In the most similar
case, I was attempting to predict adsorption in coal, which was
modeled as a collection of ring-bearing macromolecules composed of
~70-200 atoms each, for a total system size of ~6000 atoms.

To summarize, I was unable to find a combination of Monte Carlo moves
in Towhee that resulted in a realistic bulk coal density. The best I
could get via MC were densities ~30% below experimental values,
casting doubt on any adsorption predictions. In contrast, MD
simulations predicted much more realistic bulk densities but weren't
of much use in predicting adsorption.

You may have better luck with your system, but I eventually concluded
that the local nature of most MC moves weren't particularly
well-suited to my needs. I decided I needed MD to globally update or
relax the entire system while other MC moves handled the adsorption
aspect. Unfortunately, I could not find anyone giving away hybrid
Monte Carlo / molecular dynamics code. As a result, I concocted a
script that alternates using Towhee for MC moves with DL_POLY (a free
but I-don't-think open-source code) for MD. Basically, Towhee is used
to insert, remove, translate, and rotate my relatively small adsorbate
molecules while dl_poly periodically relaxes the entire system
globally. It's a work in progress and not polished, but I am willing
to share.

Cheers,
Craig

On Mon, Oct 20, 2008 at 23:05, li jianguo <lj...@ya...> wrote:
>
> Dear all,
>
> I want to simulate the adsorption of gas molecules in a polymer membrane.
> The polymer chain consists of approximately 50-100 monomers. Each monomer
> contains five-atom rings and six-atom rings (as shown in the attachment). I
> noticed that TOWHEE can deal with peptide or protein by performing
> "Configurational-Bias Protein Backbone Regrowth and side-chain Regrowth". Is
> it possilbe to move the long polymer chain full of rings in TOWHEE?
>
> Thansk very much!
>
> best regards,
> Jianguo
> Research Fellow
> Dept. Chem. & Biomoleculear Engineering
> National University of Singapore
>
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