From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 29 2007 - 16:52:02 CDT
Just to verify, you don't have any constraints in place in your
production runs?
Also, have you tried this without rigidBonds and with a 1 fs timestep,
just to see if it makes a difference?
Peter
Morad Alawneh wrote:
> *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 that value.
> 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.
>
> Morad Alawneh*
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