<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear Justin:</DIV>
<DIV> 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.</DIV>
<DIV> Thank you again for your help.</DIV>
<DIV> Sincerely: YeQing <BR><BR>--- <B>09年11月29日，周日, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> 写道：<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>发件人: Justin A. Lemkul <jalemkul@vt.edu><BR>主题: Re: [gmx-users] An unexpected behavior of rdf calculated by the g_rdf command<BR>收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>日期: 2009年11月29日,周日,上午10:57<BR><BR>
<DIV class=plainMail><BR><BR>青 叶 wrote:<BR>> Dear Lukasz:<BR>> Thank you for your reply, I have checked my *.ndx file very carefully and there are the follow words in the file:<BR>> [AU]<BR>> 1<BR>> [CL]<BR>> 2 3 4 5<BR>> [OW]<BR>> .........<BR>> 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.<BR><BR>I think you are simply missing some vital information from g_rdf -h:<BR><BR>"If a run input file is supplied (-s) and -rdf
is set to atom, exclusions<BR>defined in that file are taken into account when calculating the rdf."<BR><BR>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.<BR><BR>If these atoms are bonded, what is the purpose of calculating the RDF between Au and Cl?<BR><BR>-Justin<BR><BR>-- ========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list <A
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