We are equilibrating and running 2ns production runs of double
stranded in explicit solvent based on the turorials on the
website. At the moment I have two jobs running using
sander_classic in AMBER6.
(Note - if it is Ewald, you should be using sander in amber6.)
Would it be reasonable to also run some jobs using sander in
AMBER5 and compare the results obtained from all of the runs?
Checking is always good. You may be faced with a qualitative
decision about what difference you are willing to accept and
what you would do with an unacceptable difference.
since I am already running jobs using sander_classic what modifications
, if any, should I make to the input files for sander in AMBER5
to better draw conclusions when the comparing the runs?
This would depend on your input file.. as a first try, I suggest
using the same input file and see if it works.
Bill Ross
Received on Fri Jul 06 2001 - 13:18:23 PDT
