[gmx-users] g_velacc bug?

[Claudio J. Margulis]

Dear David, these are my conclusions so far:
I believe that replacing XX and XX for YY and ZZ gives the correct
answer and fixes the g_velacc bug.
 
The for loop should be left as it was in the original g_velacc.c code,
[i.e for(j=0; j<atndx[index[i]+1] - atndx[index[i]]; j++)]
 
Having said this, I must admit again that I know nothing about the data
structure inside gromacs so somebody who understands it should really
test that what I'm saying is correct.
 
To come to these results I had to do a lot of trjconv into gro files and
then a bunch of perl. It would be very helpful to me if I knew exactly
what goes into the trr files so that I could try to find some xdr reader
in fortran (which I am more comfortable with than C) and I could pull
out the data. 
Does anybody have a fortran program that reads trr files?
If not, can anybody point out to the xdr decoding routines in fortran?
and also to the exact data that is written into the trr files?
 
Thank you!
Cheers,
Claudio.
 
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
------------------------------------------------------------------------
-----------------
 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20031203/c22d38dc/attachment.html>