[gmx-users] DPPC equilibration problems

Santi Esteban Martin sanesmar at alumni.uv.es
Fri Nov 19 17:30:22 CET 2004

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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