[gmx-users] Diffusion Cofficient of POPC

minnale minnale_gnos at rediffmail.com
Wed Jul 16 06:45:38 CEST 2008

Hi all, 
     I have read the literature about Diffusion cofficient(Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion, Vol-125, page-204703, Journal-THE JOURNAL OF CHEMICAL PHYSICS)
then I have given command like this
 g_msd -f 5ns_popc.xtc -s .tpr -n p4.ndx -o msd_popc.xvg -lateral z
In the index file i have selceted p8 for the centre of mass and it will be  like this
[ P8 ]
   8   60  112  164 ......................

I got the diffusion cofficient value like this 
MSD gathered over 5000 ps with 501 restarts
# Diffusion constants fitted from time 500 to 4500 ps
# D[        P8] = 0.0131 (+/- 0.0190) (1e-5 cm^2/s) 

The actual D=(1-10)*10-7 cm2/s from above mentioned article but iam getting the value 1e-5 cm^2/s

I have tried in different ways with options -type z but I didnt get the value near to actual value.

Could you please tell me where I am doing mistake 

Thanks alot in advance.
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