AMBER Archive (2003)

Subject: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold

From: John D. Chodera (jchodera_at_ugcs.caltech.edu)
Date: Sat Jan 18 2003 - 03:26:12 CST

I have located what appears to be an error in the AMBER7 version of
sander. In the file newvel.f, line 58, in subroutine RANVEL, the
following line appears:

      BOLTZ = (8.31441D-3/4.814D0)*TEMP0

The conversion factor from joules to calories is incorrect. The line
should, of course, read:

      BOLTZ = (8.31441D-3/4.184D0)*TEMP0

Looks like somebody's brain was going faster than their fingers. :)

This bug would cause the system temperature to be consistently too cold
when using the VRAND flag to redraw the velocities at regular intervals.

Cheers,

- John 

-- 
John Chodera <jchodera_at_ugcs.caltech.edu>  | Mobile    : 415 577-8281
Graduate Group in Biophysics, Dill lab    | Lab phone : 415 476-8910
University of California, San Francisco   | Lab fax   : 415 502-4222