From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Thu Mar 29 2007 - 16:29:04 CDT
*Thanks Sterling, I thought I will be able to write the code without
referring to those books. I do have those books, and I will read that
part and see how fast I can understand it and write a code for it.
Yes, I do allow the lipids to move under non NPAT ensemble.
The constraint that you saw in that table was only a planer constraint
for the lipids phosphorous atoms in the z-direction, all the other
lipids atoms were free to move in 3 direction.
The reason for this is to keep PP distant as what was published recently
by Kucerka et. al. 2005, and allow the system to adjust its area under
NPgT until it reach to an equilibrium, then fix the area according to
The way I chose gamma was by doing many MD simulations with different
gamma values, and by plotting the area per head group vs gamma values, I
picked the gamma value that gave me the area per head group close to the
experimental value of the area per head group from that article.
Thus, by doing that I have PP distant and the area per head group close
to the experimental values.
What is bothering me, after 10 ns production run under NPAT, I should
have a gamma value close to what I used under NPgT, but I do not have
that besides the pressure problem.
I will get back to you with the results of the autocorrelation calculations.
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