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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