AMBER Archive (2004)

Subject: AMBER: TI with sander

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Tue Sep 14 2004 - 13:58:01 CDT

Dear all,

I have a few questions w.r.t thermodynamic integration with sander:

o Is it correct that, if atoms disappear, the backward direction can not
be simulated. I.e. the hysteresis between the forward and the backward
direction, as an error estimate, can not be computed?
How should one estimate the error then?

o What meaning do dV/dL values have for lambda=0 and lambda=1 ?

o Where in the source code can I find the paragraphs relevant for TI?

Many thanks in advance,
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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