[gmx-users] Layerwise protein-water HB Correlation

[xy21hb]

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,


Yao