[gmx-users] problem with result from g_rdf

Sheyore Omovie omovie_johnnie at hotmail.com
Sat Jan 5 03:05:29 CET 2008

Using g_dist I got the distance between the atom pair for which i need rdf.  Made a histogram, using the default bin width used in gromacs. Then divide by 4*Pi*r^2 to normalize (where r is the distance between the pair). I expect my values to agree with that from g_rdf. While the graphs are exactly alike, the values from g_rdf are greater by a small factor.
Have I missed out something in my calculation?
I would appreciate any help.

From: omovie_johnnie at hotmail.comTo: gmx-users at gromacs.orgDate: Fri, 21 Dec 2007 09:40:19 -0500Subject: [gmx-users] problem with result from g_rdf

Dear all, When I use g_rdf to find the rdf between the alpha C-atoms in my simulation, I get the usually expected result.However, when I use g_rdf to get the rdf between just the central alpha C-atoms of the two peptides (my simulation is 2 peptide in a box of water, each peptide has 3 residues), I get some really weird result: 
I get several plots that start off from a peak and gradually die off at the cut-off radius.I would appreciate any help.RegardsJohn

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