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 <[EMAIL PROTECTED]> 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 <[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]); > > > > > > 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!? > > > > 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 > === message truncated === __________________________________________________ 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