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.
________________________________________________________________________
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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