[gmx-users] Diffusion Cofficient of POPC

[Jojart Balazs]

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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