[gmx-users] Diffusion Cofficient of POPC

[David van der Spoel]

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

Aren't you getting 0.0131e-5 = 1.31e-7?

> 
> 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se