AMBER Archive (2004)

Subject: AMBER: sander_classic for cap simulations?

From: Oliver Hucke (
Date: Thu May 13 2004 - 17:43:36 CDT

Dear amber users,

I recently posted a message about the large fuctuations of the
electrostatic energy observed with a system with a solvent cap and
sander of amber8 with a non-infinite non-bonded cutoff.

After a reply from Ben Cossins I used sander_classic (of amber6) for the
same simulations in order to make use of a residue based instead of an
atom based non-bonded cutoff. The fluctuations are much smaller and the
system seems to equilibrate. The performance with a 12A cutoff is
~250ps/day which is about 4 times the performance for the corresponding
periodic system :-)

Is it possible to use a residue based cutoff with sander of amber8?
Or is the usage of sander_classic for simulations with a cap still the
way to go?
If so, should sander_classic not be part of the amber8 distribution?



Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: _______________________________________________________________

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