[gmx-users] g_velacc bug?

[David]

On Tue, 2003-12-02 at 23:00, Claudio J. Margulis wrote:
> Dear David, 
> 
> I already did that, and my impression is that it is still broken.
> 
try replacing

	for(j=0; j<atndx[index[i]+1] - atndx[index[i]]; j++) {

by

	for(j=0; j<atndx[index[i+1]] - atndx[index[i]]; j++) {



> I have a liquid that includes the ions PF6- 
> 
> Obviously P is for all purposes at the center of mass of the
> molecules.
> 
> If I compute the velocity autocorrelation function for P I get a
> function
> 
> that is totally different from the one I get for PF6-
> 
> I know the correlation function for P is right because I computed it
> separately.
> 
>  
> 
>  
> 
> Thanks for looking into this.
> 
> Claudio.
> 
>  
> 
>  
> 
> >> Hi, I’m trying to use g_velacc to compute the velocity
> autocorrelation
> 
> >> function for a set of molecules.
> 
> >> 
> 
> >> When I compute g_velacc for atoms it gives the correct answer (I
> wrote
> 
> >> my own program to check)
> 
> >> 
> 
> >> When I compute it for molecules (with option –mol and and index
> file
> 
> >> with molecules not atoms)
> 
> >> 
> 
> >> I get strange results.
> 
> >> 
> 
> >>  
> 
> >> 
> 
> >> I looked at the source code (admitedly I’m a much better fortran
> 
> >> programmer than c) but these few lines look weird to me.
> 
> >> 
> 
> >> Can anybody tell me if  line 7 to 9 they are right or not?
> 
> >> 
> 
> --please replace by YY and ZZ and test. Could you report back whether
> that
> 
> --solves the problem? I'm afraid this program is not very often used,
> and
> 
> --hence not well tested.
> 
>  
> 
> -----------------------------------------------------------------------------------------
> 
> Claudio J. Margulis
> 
> Assistant Professor
> 
> Department of Chemistry
> 
> University of Iowa
> 
> 319 CB
> 
> 319-335-0615 (office)
> 
> http://www.uiowa.edu/~chemdept/faculty/margulis/index.html
> 
> -----------------------------------------------------------------------------------------
> 
>  
-- 
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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