[gmx-users] estimation of error using ACF.

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 12 20:01:31 CET 2003

On Wed, 2003-02-12 at 16:27, Alan Wilter Sousa da Silva wrote:
> Thank you very much Dr. Spoel.
> 	I played with g_lie and find two small errors.
> 	Changing g_lie.c, I did (commentaries):
> static real lie_lj=0,lie_qq=0,fac_lj=0.161,fac_qq=0.5; /* 0.181 by 0.161*/
Actually 0.181 is now the refined value, see:

  author = 	 {J. Marelius and T. Hansson and J. {\AA}qvist},
  title = 	 {Calculation of ligand binding free energies from molecular
dynamics simulations},
  journal = 	 {Int. J. Quant. Chem.},
  year = 	 1998,
  volume =	 69,
  pages =	 {77-88}

> and
>     { "-Cqq",  FALSE, etREAL, {&fac_qq}, /* lie by fac */
This was a nasty bug. That explains why I never got any reasonable
results... I'll put it in the development version.

> 	I also noted, but I wasn't able to fix, that at lie.xvg output,
> last line has the value 0 (zero) for column Time and repeats the the last
> value for DGbind.  So when using g_analise I got error with option -ee.
> Removing that last line, g_analise works fine and then I got a err.est,
> ACF, as well the right value for average, which is a little bit different
> from what g_lie gives, certainly due to the extra datum.
> Do you think that such errors in code of g_lie.c should be corrected,
> supposed I did the right thing?  And, if you don't mind, since I'm not
> familiar to CVS, of course if you wish, would you make that corrections in
> CVS version?
> I hope to be contributing a little bit to Gromacs, although I'll never get
> to pay back all what GMX has been doing for me.
Thanks for your kind words, citing the gromacs papers does help us
though.... Obviously bug reports are also important for us. 

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. 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

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