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

traviskemper travkemp at gmail.com
Mon Apr 1 00:03:52 CEST 2013

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:

    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?


View this message in context: http://gromacs.5086.n6.nabble.com/g-dipoles-g-molecular-center-of-mass-issue-tp5006778.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list