[gmx-users] g_msd

[T. Zaraiskaya]

hello

could you give some comments about the g_msd program? When option -mol is used
how does the program calculate the diff.const?

%g_msd -f traj.trr -s topol.tpr -n index.ndx -mol -mw -lateral z

if traj.trr is used as input, i would expect to get MSD of the 
center of mass of the molecule as a function of time.
instead, the output diff_mol.xvg contains diff.constants as a 
function of molecular number..?
What are -beginfit and -endfit that the program used to fit 
a straight line and compute the diff.const?

p.s. the system i simulate is a bilayer mixture of two types 
of lipids in a water box.

thanks,
-- 
====================================
Tanya Zaraiskaya
Physics Department
University of Guelph
Guelph, ON, N1G 2W1
CANADA
email:tz at physics.uoguelph.ca
phone:(519)824-4120 x58346.