AMBER Archive (2008)

Subject: Re: AMBER: Jarzinsky relationship

From: Adrian Roitberg (
Date: Mon May 05 2008 - 09:46:53 CDT

E.M. wrote:
> Hello,
> I am doing some pulling experiments using Jarzinsky's relationship,
> the output file using AMBER9 is something like
> x xo whatever work
> My question is, do I have to substract the biasing potential after I get
> the output
> or that is taking care of by the program?. I just want to make sure I
> understand
> what is going on here.
> Regards
> E.M.


The 'wathever' in the list is the crucial factor, in fact it is the only
one one computes !

It is the external force applied by the external spring (as defined in
the input file). Basically, it is k*(x-x0)

Work is the integral of that force over the run, so there is no need to
subtract the biasing potential. The subtraction would be needed only if
work was computed from the spring energy, which is not.


                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email ============================================================================

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