>>>> Dechang Li wrote: >>>>> Dear all, >>>>> >>>>> I want to use g_rotacf to calculate the order parameter(S2, N-H bond >>>>> in >>>>>main chian). >>>>> The tool g_rotacf needs an index.ndx file that contains two vectors. >> >>>g_rotacf wants the index number of two atoms to calculate the order >>>parameter of an NH vector. You should give the index number of the atoms >>>N and H and use the option -d. Note that you have to take care of the >>>overall rotation of the molecule in the calculation. Either you remove >>>it before the calculation or you include it in the fit of the correlation >>>function. >> >> I read the manual that the index file should contain 3 atoms, i.e. (i, j, >>k). >> Is that mean I should write the index file like this: >> >> [ group1 ] >> 1 3 4 >> [ group2 ] >> 5 8 9 >> >> where 1 for atom Ca, 3 for atom N, and 4 for atom H, in a peptide?
>This will not define a vector! To follow the movement of the NH vector >(made of two atoms! the N and the H) you need only two index numbers, the >one of the N and the one of the H. Then the option -d is needed for >g_rotacf to treat the corresponding vector. Thank you for your reply! It was helpful. It was said that the index file only need 2 atoms, i.e. index of N and H. However, for the residue PRO, how to define the vector NH? >>>>>How can I make the >>>>> index.ndx file? Can I use the tool make_ndx to do this? Or I need to >>>>> write >>>>>the file manually? >>>> >>>> See http://wiki.gromacs.org/index.php/Index_File. I think you just want >>>> to write a file by hand. >>>> >>>> Mark >>>> _______________________________________________ >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>>----------------------------------------------------- >>>XAvier Periole - PhD >>> >>>- Molecular Dynamics Group - >>>Computation and NMR >>>University of Groningen >>>The Netherlands >>>----------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php