[gmx-users] asking for recommendations

[Tsjerk Wassenaar]

Hi Michelle,

What reasons do you have suggesting factors other than modelling
limitations? Is there experimental data regarding the time scale of
uncoiling? I would guess it would take longer than 20 ns. Also, you should
consider that you're looking at a single molecule. The observation of
uncoiling in vitro or in silico involves many molecules, of which one may
stay coiled for a long time (maybe the one you're looking at in your
simulation).

You might try to express the properties of your helix in terms of number of
hydrogen bonds, helix length, helix radius and helix bending, in which you
could observe trends towards more loose states, suggesting the onset of
uncoiling. But it would also be better to try and extend the simulations.

Cheers,

Tsjerk

On Dec 12, 2007 9:57 AM, michelle yap <mcy_331 at hotmail.com> wrote:

>
> Hi!
>
> I am a student currently using GROMACS (which I am new at)  for a study on
> iota-carrageenan. The starting structures used are already in a double helix
> configuration. One file contains two ten-monomer iota-carrageenan chains
> coiled into a double helix; the other two files (differing only in the
> arrangement of the helices) consist of three double helices, each helix
> consists of two six-monomer chains. These were simulated at two conditions -
> high temp and room temp - for 20 ns each. The double helix should
> theoretically uncoil. However, no such uncoiling was observed. I was tasked
> to perform analysis tools to possibly provide other "reasons" for the
> observed results apart from modeling limitations (i.e. relatively short
> length and simulation time). As of the moment, I am doing g_hbond for h-bond
> analysis. Could you please recommend other analysis tools that are likely to
> be useful in my research?
>
> Thank you!
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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