[gmx-users] estimation of error using ACF.

David spoel at xray.bmc.uu.se
Tue Feb 11 20:20:09 CET 2003

On Tue, 2003-02-11 at 15:19, Alan Wilter Sousa da Silva wrote:
> Hi List!
> I'm trying to user Linear Interaction Energy method to estimate Binding
> Free Energy.
> I use for that g_energy with -sum option besides others.
> I'm trying to use ACF ( with -fluct -fitfn exp -corr)  to estimate the
> error but, when choosing more than one group at g_energy menu I get a
> segmentation fault and programme stops at ACF calculations.  When
> choosing only one group, things work ok.  But I need to choice more than
> one since I'm investigating interactions between ligand/protein.
> It is a bug? Or am I doing something wrong about the g_energy command
> options?
there is a special program g_lie to do this kind of things. Doule check
your output, though, it is not very well tested. Error estimates are
best done by g_analyze (on your .xvg file), although knowledge of the
energy autocorellation can be useful.

> Thanks in advance,
> Cheers,
> -----------------------
> Alan Wilter S. da Silva
> -----------------------
>  Laboratório de Física Biológica
>   Instituto de Biofísica Carlos Chagas Filho
>    Universidade do Brasil/UFRJ
>     Rio de Janeiro, Brasil
> _______________________________________________
> 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.
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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

More information about the gromacs.org_gmx-users mailing list