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 < [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>:
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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