[gmx-users] Discrepancy between RDF and Hbonds results

George Patargias 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
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27

Office: +302106597568

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