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 <[EMAIL PROTECTED]> 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]); > > > > > > 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. > > > > > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- > 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 > [EMAIL PROTECTED] > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php