[gmx-users] g_order C code

Erik Marklund erikm at xray.bmc.uu.se
Thu Sep 14 15:32:31 CEST 2006 

Hi again.

I've taken a quick glace at the code, trying to figure out what the
different structures and variables are all about. Here goes...

order seem to be an array of pointers to 3D-vectors (type rvec, that
is).
ngrps is in this case actually the number of atoms in a group. Therefore
(*order)[i][XX] refers to the x-component of the order-vector belonging
to atom i.

Have a look at gmx/include/types/block.h. There toy will find some
descriptions of variables nrgrps ( = nr in block.h), index and more.

That's my interpretation of things. Still I know little about the order
parameter, so I don't know if the above makes sense or not.

Hope that helps.

/Erik

On Thu, 2006-09-14 at 05:48 -0700, priyanka srivastava wrote:
> thanks again for your prompt reply.
> 
> Okey, and I am not good at programming at all :-)
> 
> By looking at the gmx_order.c program could u tell me
> which flag is i.e. index[i] or only [i] is indicating
> the elements of a group?
> 
> Supppose there are 14 groups (i guess denoted by ngrps
> in the code) and each group in turn contains 48
> elements, so what I am interested to know is the flag
> that is associated with the second part i.e.
> individual elements.
> 
> regards,
> Pri...
> 
> --- Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 
> > 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.
> > > > > 
> > > > > 
> > > > > 
> > > > >
> > __________________________________________________
> > > > > Do You Yahoo!?
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> > _______________________________________________
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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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> > > >
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > 
> === message truncated ===
> 
> 
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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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