[gmx-users] g_order C code

[Erik Marklund]

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