[gmx-users] Problems with Jacobi diagonalization

Dayle Smith daylemariesmith at gmail.com
Wed Apr 1 17:04:46 CEST 2009

I'm working with a DNA system, and all of the routines I've worked with that
require Jacobi diagonalization (g_covar, g_rms, etc) fail with the "Too many
iterations in routine JACOBI" error. I'm using gromacs-3.3.3 with ffamber99
on the NCSA Mercury cluster. I've searched the archives, and I've found
several entries in which users are advised to check that the coordinates in
the trajectory and structure files match (mine do). I've also tried running
covariance analysis on a small ligand molecule, and I get the same error. I
can get g_covar to work with -nofit, but then I can't run g_anaeig.

I'm eagerly looking forward to your suggestions!

Have a great day,
Dayle Smith
Department of Physics
Whitman College
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