[gmx-users] [gmx-users]g_velacc bug?

[David]

On Thu, 2003-12-04 at 04:04, Claudio J. Margulis wrote:
> Dear David, I did try changing the code as you suggested. But it gave
> the wrong results. Let me explain,
> 
>  
> 
> I wrote a bunch of  programs to take trajectories in .gro format
> (which I obtained by trjconv –nojump - … from the original trr ). For
> each of the PF6- molecules in the box I computed the trajectory of the
> center of mass and proceeded to compute the averaged time correlation
> function of it with another little program I wrote.
> 
>  
> 
> I compared this result to
> 
> 1) unchanged g_velacc
> 
> 2) changing XX XX for YY ZZ
> 
> 3) changing XX XX for YY ZZ and modifying the loop as you suggested.
> 
>  
> 
> My pedestrian computation gives exactly the same result as in 2, 1 is
> a little different, and 3 is totally different.
> 
>  
> 
> This is my understanding of the reason why the cm vac and the p vac
> are so widely different:

OK, I looked once more, and now it seems that the code is correct indeed
in case 2, as you say. I was confused by the double indexes. Anyway, I
fixed the other bug (1->2) in the code, thanks for reporting it.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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