[gmx-users] g_hbond in/output

Wed Dec 20 17:34:22 CET 2006

I have some questions about g_hbond option. 
1) My system consists of a protein molecule (a capped 1 alanine residue) (CH3-CO-ALA-NH-CH3) and 250 water molecules. After selecting the g_hbond option, it says that protein molecule consists of 12 elements; however, it consists much more elements as it can be seen. Could you explain the reason behind it?
2) In order to investigate the Hydrogen bonds formed between water molecules and the protein, should I select the protein and solvent option? I selected like this, but I encountered with the following error:
Range checking error:
Variable gx has value -3. It should have been within [ 0 .. 5 ]
Please report this to the mailing list (gmx-users at gromacs.org)
3) In the output file of hbnum.xvg, there are three columns.I think, the first column represents the time step, the second column the number of hydrogen bonds. What about the third column?
Thanks in advance

Department of Computational Science and Engineering
Koc University, Istanbul 

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