[gmx-users] Layerwise protein-water HB Correlation

xy21hb xy21hb at 163.com
Wed Aug 27 20:53:07 CEST 2014

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Dear all,

I am doing a layerwise hydrogen bond lifetime correlation function (HBCF) for lysozyme-water system.
I use "trjorder", "-r" to select the water within some distance (5 A) to the protein, and "-o" to generate a new trajectory.
However, when g_hbond the trajectory, the HBCF shows very small (10e-4) values, which is certainly not true compared to HBCF between the protein and all water molecules.
I wonder what is a correct way to select water near protein for further analysis.

Many thanks,


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