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

青 叶 yeqing_121 at yahoo.com.cn
Mon Nov 30 03:08:53 CET 2009

Dear Justin:
      Thank you very much for you advise, it seems I should read the manual more carefully. The Au and Cl atoms are formed a cluster [AuCl4]- and there are bonds between Au and Cl.
      Thank you again for your help.
                                                                                                      Sincerely: YeQing    

--- 09年11月29日,周日, Justin A. Lemkul <jalemkul at vt.edu> 写道:

发件人: Justin A. Lemkul <jalemkul at vt.edu>
主题: Re: [gmx-users] An unexpected behavior of rdf calculated by the g_rdf command
收件人: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
日期: 2009年11月29日,周日,上午10:57

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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