[gmx-users] g_dipoles -g molecular center of mass issue

[traviskemper]

I am calculating the < cos > between molecular dipoles, and I am getting
strange values for the molecular center of mass distance (r). So I ran
a test on a simple dimer system:

dips
 4
    1DIP     C1    1   0.000   0.000   0.000
    1DIP     H1    1   1.000   0.000   0.000
    1DIP     C1    1   0.000   1.000   0.000
    1DIP     H1    1   0.000   1.000   1.000
   10    10    10

with +/- 0.1 for H1 and C1 respectively, and a mass of 1.0 for each atom. By
running g_dipoles -g on the above structure I get a value of 0.01 for the
value of r. However, when I place H1 of the first molecule at 0.0 0.0 1.0, I
get the correct value of r. Also when I try to set the maximum distance with
-rcmax, I get the error "No data in the cmap." Am I missing some key words,
or some reference files?

Thanks,
Travis



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