[gmx-users] About Lateral Diffusion of Lipids

[Justin Lemkul]

On 1/16/13 6:18 AM, vidhya sankar wrote:
>
>
> Dear Justin Thank you for your Previous reply
>
> I am Following your Protein Lipid Tutorial When I do the msd analysis For  protein in DPPC lipid-water Bilayer in lateral Z direction  using P8 atoms as index  Then  I have Got the Following Output      Is the Following My  Out put is Reasonable or Not?

Literature searching and reading previous studies (both computational and 
experimental) will tell you whether it's reasonable or not.

> Used 101 restart points spaced 10 ps over 1000 ps
>
> Fitting from 100 to 900 ps
>
> D[        P8] 0.0544 (+/- 0.0057) 1e-5 cm^2/s
>

Metrics like these require long simulations (tens or hundreds of ns) to be reliable.

> What Is Lateral Diffusion of Lipids ?  Its Value for Membrane Protein (output ) indicates What ?
>

If you don't know what it is, why are you measuring it?  Again, do some reading.

> Is there is Limiting (upper, Lower ) Value For Every System ?  How could I come to a conclusion That  My Value  of My  Diffusion Coefficient is Reasonable or Not
>

Same as above.  I'm not going to do your homework for you.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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