[gmx-users] Error estimation with TI

[David van der Spoel]

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?
>
> Regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>         mgoette2[at]gwdg.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?
>>>
>>> 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.
>>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.


-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++