[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Mon Oct 17 13:56:17 CEST 2011


As the consequence the correct orientation of the peptide in the membrane as
well as futher solvation are caused many questions :)

Firsly, following by tutorial guide I've done orientation of KALP peptide in
the membrane by

1- perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
2- minimization
3- perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

4- minimization

after six iterations of the  3rd and 4th steps I've obtained 6,5 nm^2
value for the area per lipid

Next I've done solvation of my protein ( including big vdv radii for carbons )

Finally my sytem is consisted of 70000 atoms. I think that it's too
big ammount of water molecules for such small protein like KALP

so its seems that i've done some mistakes-
1- During shrinking of my peptide- I think that obtained structure
(http://www.sendspace.com/file/wenkf4) consist of too big distances
beetween peptides so it should be futher shrinked.

But how many iterations must be? I've found in the tutorial that 65
A^2 is good value for that system. But maybe I've used wrong
parametries in the pl program?

2- Or maybe too many waters are moved within the membrane in spite of
increased VDV radius for carbon atoms. So what I should do for the
excluding all unnecessary water from my structure?

E.g I want to simulate hydrophobic effect. What length of that
simulation must be ?
How I can evaluate the ammount of water before and after simulations?
Finally, What other options of Genbox could I use for preventing
insertion of water into my membrane ?

Thank you for your help,

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