[gmx-users] About Lateral Diffusion of Lipids
jalemkul at vt.edu
Wed Jan 16 12:24:27 CET 2013
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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