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

[Qiao Baofu]

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





2006/9/15, Qiao Baofu < 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
**********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060915/9806b130/attachment.html>