[gmx-users] Re: question about g_rdf -com & a little mistake on make_ndx

[David van der Spoel]

Qiao Baofu wrote:
> Hi,
> I am using Gromacs 3.3.1. In the help file of make_ndx, it is said that  
> "splitres" is to split group into residues, and "splitat" is to split 
> group into atoms. But after I use them two, I found they are opsite. see 
> the following example
> 
>  > splitres 3
> Splitting group 3 'MIL' into atoms
> 
>  > splitat 3
> Splitting group 3 'MIL' into residues
> 

printing is wrong, result is right. this is already fixed in CVS, but 
thanks for reporting it anyway.
> 
> 
> 
> 
> 2006/9/15, Qiao Baofu < qiaobf at gmail.com <mailto:qiaobf at gmail.com>>:
> 
>     Hi All
> 
>     I have 2 questions about using g_rdf -com: 
>     1. In the manual, it is said that when -com option used, the rdf is
>     calculated with respect to the center of first group. My question is
>     that,  if i want to calculate the rdf of the COM of two groups, how
>     to do it?
>     2. In my mind, for single-atom,  the COM should just be the center
>     of it. Therefore, if I calculate the rdf of two single-atom groups
>     WITH and WITHOUT -com option, the result should be the same.
>     However, it is not that case. I calculated the rdf of H-Cl in these
>     two methods, and got quite different result!! see the attachment. Why?
>      
> 
>     PS: I use gromacs 3.3.1.
> 
>     -- 
>     Sincerely yours,
>     **********************************************
>     Baofu Qiao, PhD
>     Frankfurt Institute for Advanced Studies
>     Max-von-Laue-Str. 1
>     60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
>     **********************************************
> 
> 
> 
> 
> -- 
> Sincerely yours,
> **********************************************
> Baofu Qiao, PhD
> Frankfurt Institute for Advanced Studies
> Max-von-Laue-Str. 1
> 60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
> **********************************************
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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