[gmx-users] Question about g_rdf under Version 3.3.3:

qiaobf qiaobf at gmail.com
Fri Oct 10 05:24:13 CEST 2008

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!

Baofu Qiao
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