[gmx-users] g_order C code

[priyanka srivastava]

Thank you for your reply.

I am also curious to know if this is the right way of
doing it. I am not sure of the changes that I have
made in the code.

Any suggestions on that please? 

Since, when I say "make install" it gives the
following error:

cc -DHAVE_CONFIG_H -I. -I. -I../../src
-I/usr/X11R6/include -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3
-fomit-frame-pointer -finline-functions -Wall
-Wno-unused -malign-double -funroll-all-loops -MT
gmx_order.lo -MD -MP -MF .deps/gmx_order.Tpo -c
gmx_order.c -o gmx_order.o
gmx_order.c: In function `calc_order':
gmx_order.c:251: called object is not a function
gmx_order.c:252: called object is not a function
gmx_order.c:252: called object is not a function
gmx_order.c: In function `order_plot':
gmx_order.c:300: `i' undeclared (first use in this
function)
gmx_order.c:300: (Each undeclared identifier is
reported only once
gmx_order.c:300: for each function it appears in.)
gmx_order.c:301: called object is not a function
gmx_order.c:302: called object is not a function
gmx_order.c:302: called object is not a function
gmx_order.c:303: called object is not a function
gmx_order.c:304: called object is not a function
make[2]: *** [gmx_order.lo] Error 1
make[2]: Leaving directory
`/home/histidine/gromacs/gromacs-3.3/src/tools'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory
`/home/histidine/gromacs/gromacs-3.3/src'
make: *** [install-recursive] Error 1


thanks and regards,
Priyanka.




--- Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> On Thu, 2006-09-14 at 02:21 -0700, priyanka
> srivastava wrote:
> > Dear Gromacs users,
> > Hie,
> > 
> > I am calculating the order parameters for a
> bilayer
> > patch using g_order analysis tool in gromacs
> version
> > 3.3.
> > 
> > I have a total of 48 elements in the patch and I
> want
> > the order parameter value for each and every
> element
> > i.e. a total of say 48 values for order parameter
> > alongwith the average which g_order reports. 
> > 
> > I tried to fiddle with the code too and tried
> changing
> > the following section as follows:
> > 
> > /* average over frames */
> >   for (i = 1; i < nr_tails; i++) {
> >    /* svmul(1.0/nr_frames, (*order)[i],
> > (*order)[i]);*/
> >     fprintf(stderr,"Atom %d Tensor: x=%g , y=%g,
> > z=%g\n",i,(*order)(index[i])[XX],
> >             (*order)(index[i])[YY],
> > (*order)(index[i])[ZZ]);
> > 
> > 
> > and also:
> > 
> > sprintf(buf,"Deuterium order parameters");
> >     slOrd = xvgropen(cfile,buf, "Atom", "Scd");
> > 
> >     for (i = 1; i < nr_tails; i++) {
> >       fprintf(ord,"%12d   %12g   %12g   %12g\n",
> atom,
> > order(index[i])[XX],
> >               order(index[i])[YY],
> > order(index[i])[ZZ]);
> >       fprintf(slOrd,"%12d   %12g\n", atom, -1 *
> > (0.6667 * order(index[i])[XX] +
> >                                                 
> 0.333
> > * order(index[i])[YY]));
> > 
> > The problem is I am not sure if that is the right
> way
> > of doing this. Please suggest me something. Also
> once
> > these changes have been incorporated in the C
> program
> > how do I generate the exe of g_order. Gcc gives
> many
> > undefined errors.
> 
> In src/tools: make g_order
> It may require that various libraries are already
> compiled, which is why
> you should build all of gromacs once too (in gmx:
> make install). Having
> done that once, make g_order should do the trick I
> think.
> 
> > 
> > Please suggest me something,
> > regards,
> > Priyanka.
> > 
> > 
> > 
> > __________________________________________________
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> -- 
> Erik Marklund, PhD Student, Molecular Biopcysics
> group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,          75124 Uppsala,
> Sweden
> phone: +46 18 471 4537          fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> 
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