Hi all, Recently, I post one question about g_rdf under Version 3.3.3. After discussing with Florian Dommert, and rereading the code of gmx_rdf.c, I have the following results: 1. -nocom -rdf atom is reliable; 2. -com calculates the com of the WHOLE first group!, not the com of the molecules/residues of the first group; 3. Only when -nocom and -rdf atom are combined, the intramolecular exclusion is considered; 4. RDF of multi-atoms/molecule(-nocom)---multi-atoms/molecule(-rdf mol_com) is different from RDF of multi-atoms/molecule(-nocom)---single-atom/molecule(-rdf atom), in which the single-atom is the center of the multi-atoms. Something strange!!! Example: rdf[OAA_OAB_OAC_OAD(-nocom)---CAH_CAC_CAB(-rdf mol_com)] is quite different from rdf[OAA_OAB_OAC_OAD (-nocom)---NAI(-rdf atom)], in which NAI is the center of CAH_CAC_CAB.
>From these results, it seems that there might be a bug in the code. Or maybe >there are some misunderstanding for me! If any one has any suggestion about >it, thanks in advance! regards, Baofu Qiao
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