[gmx-users] [gmx-users]g_velacc bug?
spoel at xray.bmc.uu.se
Thu Dec 4 06:17:01 CET 2003
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 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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