Hello all I would like to plot mean square displacement of hydrogen atoms of protein versus temperature (in order to get dynamical transition temperature). I am using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o *.xvg) . I am getting following curves as uploded in :
http://s903.photobucket.com/user/nidhikatyal1989/media/msd_fig1_zpsc293a5ab.jpg.html How should I plot msd value versus temperature? Is it reasonable enough to take average over 2 ns (linear part) and discard the rest? Moreover, I suspect there is something wrong in the curves too since they are increasing first, reaching saturation and again increasing (last part is unexpected). Actually I am trying to reproduce the results of following paper: THE JOURNAL OF CHEMICAL PHYSICS 130, 135101 2009, FIG 9 (a) My values are also deviating by larger amount. Am I doing something wrong? Please help. Thanks Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
