[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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