[Spam: ***** SpamScore] [gmx-users] DPPC equilibration problems

[David L. Bostick]

Hello,

Try the Berendsen scheme for temperature and pressure only in the
z-dimension for ~0.5-1.0 ns:

coupl                  = berendsen
pcoupltype              = anisotropic
tau_p                   = 0.5
compressibility         = 0.0 0.0 4.5e-5 0.0 0.0 0.0
ref_p                   = 1.01 1.01 1.01 1.01 1.01 1.01

If you like, you can freeze the lipids and then use the above scheme for
even less simulation time ... say 200-500 ps.

Then go back to a regular scheme

pcoupl                 = Parrinello-Rahman
pcoupltype              = anisotropic
tau_p                   = 2.0
compressibility         = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
ref_p                   = 1.01 1.01 1.01 1.01 1.01 1.01

You probably did not need to entirely resolvate the membrane. It might have
been better to simply extend the box and add a slab of water above the
existing water.  All the dimensions are expanding in order to compensate
for a sudden loss of density. The above method should work to keep the
membrane area constant while the water quickly equilibrates.

David

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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On Fri, 19 Nov 2004, Santi Esteban Martin wrote:

>
> Dear list
>
> I am simulating 128DPPC(tieleman's system).
> I resolvated it because I wanted a bigger Z dimension(8nm).
>
> Basically, I used:
>
> tau_p               =  1.0      1.0     1.0     0       0       0
> compressibility     =  4.5e-5   4.5e-5  4.5e-5  0       0       0
> ref_p               =  1        1       1       0       0       0
>
> with PME and integrator step either 2fs or 5fs.
> Over 5ns simulation Area/lipid equilibrated as reported by tieleman
> and  M. Patra & M. Karttunen, and other basic properties like order
> parameters or density match as well. But I got the following situation:
>
> 1) Z dimension decrease from 8 to 7 nm. Previously to MDs I removed
> water molecules from a slab of 1 nm from the center of the
> bilayer(around 800 molecules). The decreased is even bigger if I remove
> a slab of 2nm, so I suppose the Z system dimension decreases as it has
> to refill some gaps and reach the set ref_p.
> Is it normal or I do something wrong?
>
> 2) The X and Y dimensions get far apart. I mean, the X goes from 6.5
> to 5.5 and the Y dimension from 6.5 to 7.5. Are this sort of deviations
> somehow acceptable? I wonder whether this effect might be introduced by
> some periodicity artefact related of using PME-PBC.
> Using semiisotropic pressure coupling I supposse it could be fixed,
> whether it is in fact an artefact, which I am no sure.But I plan to
> put a peptide on the interface so I think anisotropic pressure would be
> better to simulated the effect of the peptide( am I right ? ) because
> the peptide on the interface bilayer wont affect the membrane
> isotropically, thought about X-Y dimensions, because it is not isotropic
> in X-Y dimensions.
>
> Let me know about your experience.
> Thanks !
>
>
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