[gmx-users] Error estimation with TI
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jan 17 19:37:22 CET 2006
Maik Goette wrote:
> Thank you David
> I am aware of the fact, that FEP seems to be the better way.
> I just would like to compare both methods for my system.
> Nevertheless another question concerning FEP:
> The values in dgdl.xvg have to be treated somehow, I suppose. ;)
> I am not sure, if those values are "real" dG- or still dG/dl-values.
> Can you tell me, how to treat those values properly, to get the
> correct dG for each lambda run?
> And how to treat the dGs from the different lambda runs to get one
> overall dG?
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Tel. : ++49 551 201 2310
> Fax : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
> David van der Spoel wrote:
>> 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.
dg/dl, it depends on what your lambda means.
>>> 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.
Take the piece of the dgdl curve that is equilibrated and run g_analyze
-ee on it.
>>> But somehow, the delta lambda has to be included, not?
>> 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.
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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://xray.bmc.uu.se/~spoel
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