[gmx-users] Some questions about free energy calculation

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 15 20:08:13 CET 2002

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
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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