[gmx-users] Some questions about free energy calculation

[David van der Spoel]

On Tue, 15 Jan 2002, David L. Bostick wrote:

>That is something the other David may be able to answer with more
>confidence.  I have always been unsure of this.  So, I can offer the
>following 2 cents..  In the past, I have always taken the dgdl.xvg file
>output by doing FEP with mdrun, transformed the x-axis from units of time
>to units of lambda, and integrated it numerically just to be on the safe
>side.
That is also correct, if you do it slow enough (the so-called slow-growth 
algorithm), but it has the disadvantage that you can not check
equilibration at each point.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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