Dear all, I have run a 100ns simulation of protein. I want to calculate the generalized order parameters S2 for N-H. It was said that to calculate S2, the overall motion should be subtracted first. How can I subtract the overall motion? Can I use the command 'trjconv' to fit the protein to a reference strucutre firstly, and then calculate S2 using command 'g_rotacf'? If YES, what the reference structure is? The average structure in the trajectory?
Best regards, 2009-3-3 ========================================= Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn ========================================= _______________________________________________ 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