[gmx-users] g_hbond and index

Ricardo O. S. Soares rsoares at fcfrp.usp.br
Thu Feb 13 20:50:30 CET 2014

Dear users, 

By using the same trajectory and selection, I'm performing two analyses, one with -merge and another with -nomerge flag. 
With -nomerge, the xpm file has 72 lines of HB existence, the same number of pairs in the index file (h-bonds section), whereas with -merge, the entries on both files are 54. 
So I'm assuming that the n-th line of the xpm file relates to the n-th entry of the ndx h-bond block, am I right? 

If so, this rule, however doesn't apply to the full extent of my example files, where the same occupancy is described by different atoms (from different pairs) in the ndx files. Did anyone ever also found that? 
Additionally, i detected that in the index file (-nomerge) some atoms feature in the acceptor section (i.e [ acceptors_Protein ]) and not in the acceptor column in the [ hbonds_Protein] section. 

I appreciate any thoughts on this matter, 



Biological Chemistry and Physics 
Faculty of Pharmaceutical Sciences at Ribeirão Preto 
University of São Paulo - Brazil 

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