[gmx-users] Error estimation with TI

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 17 13:34:34 CET 2006

Maik Goette wrote:
> Dear all, dear David
> Again a question concerning error estimation.
> This time it's due to thermodynamic integration.
> When I simulate my system, let's say 5 ns, from lambda 0 to 1, I get my 
> dG/dl values.
> At the moment, I am simulating both directions (0->1 & 1->0), integrate 
> over both, and the difference between my back and forth sims is the 
> error estimate.
> But I think, one should use a method, similar to FEP, to "guess" the 
> error from the dg/dl-data, maybe also with generating blocks with regard 
> to the autocorrelation.
> But somehow, the delta lambda has to be included, not?
> Regards
A much better method is to simulate at e.g. 20 discrete lambda points, 
check equilibration at each point individually and also get the error at 
each point. You then finally integrate numerically. Since you check 
equilibration at each point there is no need to do a reverse sim. as 
well. Note that it may be good to check the spacing of points, in 
particular close to 0 and 1.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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