VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jan 05 2007 - 18:09:22 CST

On Fri, 5 Jan 2007, OMAR NABEEL ALY DEMERDASH wrote:

OD> Hello,

hi omar!

OD> I tried to use the GUI and the tcl command 'measure gofr' for
OD> measuring g(r) between sodium ions and the protein alpha carbons and
OD> got the nonspecific error message: 'measure gofr: error during g(r)
OD> calculation'. What would be a common cause of a failure to
OD> calculate g(r)? I should mention that I am running VMD1.8.5 on a

there has not been a lot of feed back on that plugin to identify
a common failure. please have a look at the VMD console window
for additional error messages. the GUI script can only detect,
that there was an error somewhere in the lowlevel (compiled, not
scripted) function in VMD, but there is (currently) no way to
know which one.

other than that, please let us know:
- what kind of trajectory data do you have?
- what kind of flags did you activate/deactivate when trying
  to compute the gofr?

OD> Mac OS X version 10.3.9, and the VMD webpage said that VMD1.8.5 is
OD> for versions 10.4.5 and later. VMD1.8.5 seems to be running OK for
OD> basic things like loading molecules. Would the performance of
OD> certain newer utilities, such as measure gofr, be affected by the
OD> version of Mac OS X that vmd is running on?

it always is a bit dangerous to run a binary that was compiled on
a newer release of an OS on an older version, but if VMD runs at
all, i would not expect any significant significant side effects.
measure gofr is a compiled in function (not a plugin) and the GUI
plugin is a Tk/TCL script.

cheers,
   axel.

OD> Thanks,
OD> Omar Demerdash
OD> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.