[gmx-users] g_ hbond on two peptides

Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw
Tue Jun 1 12:37:31 CEST 2010


I use g_hbond to analyze the system with two peptide.
And I introduce the ndx file which include two group for the two 
peptides respectively.
For the first prompt of g_hbond, I choose the group of the first peptide.
For the second prompt, I choose the other peptide.

I got the data that announced 4 H-bonds were found.
And then I use rasmol to check, I found there are 2 intra-H-bonds in 
first peptide and 2 intra-H-bonds in the second.
There are no inter-H-bonds between two peptides in my system.

It's strange since I had selected different group to analyze when 
g_hbond promted.
How should I do to exclude the intra-H-bond on one peptide?


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