[gmx-users] g_msd

minnale minnale_gnos at rediffmail.com
Mon Jul 14 16:01:44 CEST 2008

Hi Users, 
    I have calculated lateral diffusion cofficient of POPC bilayer which ran the simulation for 5ns. 
The command line is
 *g_msd -f 5ns_popc.xtc -s .tpr -o msd.xvg -lateral z 
 selected POPC system for calulation of msd
at the end of the run showed like this

"Used 501 restart points spaced 10 ps over 5000 ps

Fitting from 500 to 4500 ps

D[      POPC] 0.0218 (+/- 0.0244) 1e-5 cm^2/s"

Could you please tell me 
1. The input files I have given whether correct or not.
2. The 'D' value which got is correct or not?
3.what's the experimental value?
Thanks in advance.
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