[gmx-users] mean square displacement

Nidhi Katyal nidhikatyal1989 at gmail.com
Tue Sep 9 15:24:31 CEST 2014

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 :


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

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.


More information about the gromacs.org_gmx-users mailing list