[gmx-users] hbhelix,hbond,hbnum files

Fri Jan 12 00:19:48 CET 2007

I have the following problem: My system consists of a capped three-alanine residues embedded in a box with 750 water molecules. I want to analyze the hydrogen bonds formed in each frame. In this respect, I used the -hx option to investigate the exact contributors of  the hbonds in each frame since its columns give the corresponding residue pairs of the hbonds. At the same time, I used the -hbn option, and got the corresponding index file. In the hbhelix.xvg file, the n-n+2,n-n+3, and the n-n+4 columns were empty although the hbond.ndx file indicated that there were hbonds between the n-n+2,n-n+3,and the n-n+4 residue pairs, so I understood that the caps were not taken into account  when calculating the hbonds for the helix. Relying on such differences, I expected to see some differences between these two files (hbhelix.xvg and hbnum.xvg), but this was not the case, they were the same. The hbonds between the mentioned residue pairs above were not included in the hbnum.xvg file  although they were included in the hbond.xvg file. Why is this the case? Why are there any differences? 
Thanks in advance! 

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