AMBER Archive (2004)

Subject: AMBER: sander_classic for cap simulations?

From: Oliver Hucke (ohucke_at_u.washington.edu)
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?

Best,
Oliver 

-- 
_______________________________________________________________

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: ohucke_at_u.washington.edu
_______________________________________________________________

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