[gmx-users] asking for recommendations

michelle yap mcy_331 at hotmail.com
Wed Dec 12 09:57:26 CET 2007


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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