[gmx-users] Discrepancy between RDF and Hbonds results
gpat at bioacademy.gr
Sun Jul 28 19:15:59 CEST 2013
I am trying to analyze the interactions between an OH group of 8
(identical) drug molecules with water
1) I do an Hbonds analysis by running g_hbond with an index file
containing the OH of all drug molecules as the first group and all water
molecules as a second group.
The average Hbonds from the hbnum.xvg plot is ~4.8. If divide this by 8
(the number of molecules), we get 0.6/molecule
2) I calculate the RDF using exactly the same two groups (OH of all drug
molecules and water). But the integration of the RDF yields 0.
I run g_rdf with the default -rdf option (atom).
How is this disagreement can be explained?
Dr. George Patargias
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
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