Dear Minnale,
As far as i know, at least 100ns simulation should be performed in order
to obtain the correct diffusion coefficient for lipids. I think, if you
performed 5 ns it is too short.
Hope this helps.
balazs
minnale wrote:
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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