Hi Michelle,<br><br>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).
<br><br>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.
<br><br>Cheers,<br><br>Tsjerk<br><br><div class="gmail_quote">On Dec 12, 2007 9:57 AM, michelle yap <<a href="mailto:firstname.lastname@example.org">email@example.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>Hi!<br><br>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?<br><br>Thank you!<br>
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>
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