[gmx-users] An unexpected behavior of rdf calculated by the g_rdf command

Justin A. Lemkul jalemkul at vt.edu
Sun Nov 29 03:57:22 CET 2009

青 叶 wrote:
> Dear  Lukasz:
>        Thank you for your reply, I have checked my *.ndx file very 
> carefully and there are the follow words in the file:
> [AU]
> 1
> [CL]
> 2 3 4 5
> [OW]
> .........
> so I think  atom indexes for AU & CL really present there, I have 
> produced the yqq.ndx file by the "make_ndx" command from a *.tpr file, 
> and choiced the option "t" (atom type) when defining the defferent 
> groups,  By the way, I built the *.ndx file after my simulation carried 
> out, and use the "grompp" command to rebuilt the md.tpr file to add the 
> index information in it, I think "make_ndx" won't write anything into 
> the *.trr file, is there any problem in my operation? Can anybody help 
> me? Thank you very much.

I think you are simply missing some vital information from g_rdf -h:

"If a run input file is supplied (-s) and -rdf is set to atom, exclusions
defined in that file are taken into account when calculating the rdf."

Are the Au and Cl atoms bonded to one another?  If so, what do you have nrexcl 
set to?  If the Au-Cl interaction is intramolecular, the Au and Cl are 
considered part of the same molecule and thus g_rdf ignores them!  Hence the zeroes.

If these atoms are bonded, what is the purpose of calculating the RDF between Au 
and Cl?



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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