[gmx-users] g_order C code

[priyanka srivastava]

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.

Please suggest me something,
regards,
Priyanka.



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