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

[青 叶]

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.
        Best Wishes!
                                                                                                     Sincerely:YeQing 
--- 09年11月27日，周五, Lukasz Cwiklik <lukasz.cwiklik at uochb.cas.cz> 写道operation：


发件人: Lukasz Cwiklik <lukasz.cwiklik at uochb.cas.cz>
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27日,周五,下午10:06


On Fri, Nov 27, 2009 at 6:40 AM, 青 叶 <yeqing_121 at yahoo.com.cn> wrote:
>
> Hello all gmx-users:
>        I have run a 100ns long MD simulation, the system is HAuCl4 acid solution, which contains one [AuCl4]- cluster and 503 water moleculars, and calculated the rdf by using the g_rdf command as follow:
> g_rdf -f yqqmd.trr -s yqqmd.tpr -n yqq.ndx -o rdf.xvg -cn cn.xvg -rdf atom
> I have defined the groups of AU CL OW H in the yqq.ndx file, and calculated the rdf of Au-Cl, but strangely, all the function value is zero (my box vector is 2.5nm):
> # This file was created Thu Nov 26 10:58:07 2009
> # by the following command:
> # g_rdf -f yqqmd.trr -s yqqmd.tpr -n yqq.ndx -rdf atom -o rdf.xvg -cn cn.xvg
> #
> # g_rdf is part of G R O M A C S:
> #
> # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
> #
> @    title "Cumulative Number RDF"
> @    xaxis  label "r"
> @    yaxis  label "number"
> @TYPE xy
> @ subtitle "AU-CL"
>          0          0
>      0.002          0
>      0.004          0
>      0.006          0
[...]
> then I used the ngmx command to observe the trajectory file of the whole simulation, and indeed see there are four Cl atom around Au atom, (generally speaking, four Cl atoms are at the same plane and form a square, Au is in the center of this square, with a Au-Cl bond length of about 0.228 nm), but I have no idea why the rdf can not reflect the existence of Cl atom around Au?? Can anyone help me on this problem? I will very grateful for your help.
>
> Besides this problem, my Au-OW rdf seems strange also, the second peak, which corresponding to the second hydrated shell, is bigger than the first one. To my konwledge, the second hydrated shell is more "disorded" than the first one so the second rdf peak, generally, is lower and broader than the first one. I guess I had made some mistake in the calculation, but I do not know where is the mistake, does anyone meet this situation ever before?
>
> Any suggestions will be very grateful.
> My English is not good, please forgive my awkward expression.
> Thank you!
>                                                                                                     Sincerely: YeQing
> ________________________________
> 好玩贺卡等你发，邮箱贺卡全新上线！


Dear YeQing,
Regarding zeros in rdf results - can you please check how your yqq.ndx
file looks like, I mean, are atom indexes for AU & CL really present
there?
(Btw, it would be more convenient if you do not paste so many zeros
from your rdf results.)

Best,
Lukasz

--
Lukasz Cwiklik
http://cwiklik.wordpress.com
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