[gmx-users] g_order C code

Erik Marklund erikm at xray.bmc.uu.se
Thu Sep 14 14:18:25 CEST 2006 

I have never done any lipid order stuff and I don't know that much about
the underlying theory, so the only help I can offer concerns progamming
only.

It seems I have a different version of gmx_order.c, where the
problematic parts of the code are around lines 448 and 497. I think,
however, that I have found the faulty code. See below.

On Thu, 2006-09-14 at 04:44 -0700, priyanka srivastava wrote:
> 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]);
> > > 

I think that (*order)(...) makes the compiler try to call the function
*order. Since it is in fact not a function, it causes an error. Use
square brackets for indexing: (*order)[...]. If I'm right, this causes
the error messages for line 251 and 252.

> > > 
> > > 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]));
> > > 

Indeed, i is undefined in order_plot. And once again you use parentheses
for indexing. This causes the remaining errors.

> > > 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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-- 
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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