[gmx-users] DPPC equilibration problems
Santi Esteban Martin
sanesmar at alumni.uv.es
Fri Nov 19 17:30:22 CET 2004
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.
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