[gmx-users] How to use g_rdf with -com?

David van der Spoel spoel at xray.bmc.uu.se
Wed May 17 21:47:31 CEST 2006

C. D. Poon wrote:
> In the Gromacs tutorial, the  radial distribution function of 216 water 
> molecules in a box can easily be calculated by g_rdf around the oxygen 
> atom of the water molecule.  It is straight forward to use the index 
> file with one group (OW) in it for the calculation.
> I have a box of benzene.  As you can imagine, I must use the center of 
> mass of benzene to calculate the radial distribution function.  However, 
> I do not seem to understand how to use the -com option in the g_rdf 
> command.  Can anyone share your experience in using g_rdf with -com option?
It only computes COM of the central group. What you want is not implemented.

> Thanks in advance,
> CD Poon.
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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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