[gmx-users] g_gyrate

Marc Baaden baaden at smplinux.de
Fri Oct 10 16:54:01 CEST 2003


FYI, there seems to be a bug in g_gyrate (from gmx3.1.4 - haven't tried
the CVS version) when using options  "g_gyrate -p -q ...". R itselfs seems
ok, but rx ry and rz are completely off (roughly a factor of 10).

NB for the flags:
      -[no]q   bool     no  Use absolute value of the charge of an atom as
                            weighting factor instead of mass
      -[no]p   bool     no  Calculate the radii of gyration about the principal


>>> David van der Spoel said:
 >> > The values it gives out are the radius of gyration and the principle
 >> > radii of gyration; rx, ry and rz.  I would assume that r is an average
 >> > radius of gyration.  However, that does not appear to be the case as
 >> > the values that I am getting for r are larger than rx, ry and rz.  Any
 >> > insight?
 >> r = sqrt(rx^2+ry^2+rz^2)
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217

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