[gmx-users] MSD calculation

2016-01-08 Thread ?????? 
Hi GMX users:

I did a simulation of a bilayer, and I would like to calculate the diffusion 
coefficent of lipids by g_msd command.

I used the following command:
g_msd -s *.tpr -f *.xtc -n index.ndx -beginfit xx -endfit xx -trestart xx -o 
msd.xvg
I have 144 lipids in one leaflet. I am wondering what is the msd plot I got. To 
my understanding, the MSD was calculated based on the move of the center of 
mass of each lipid molecular, right? Or the MSD was calculated based on the 
move of all of the atoms I selected?
There is an option -ngroup, what does this option mean?
Thanks very much, I am really appreciate for any help. 

Cheers, 
RXG
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[gmx-users] msd calculation

2015-02-11 Thread mah maz 
Dear All,

I want to calculate msd for a group of atoms of my system in different
directions (x, y and z). What is the exact difference between -type,
-lateral and -ten in g_msd command? which one should I use?

Thank you!
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