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Methodological problems in pressure profile calculations for lipid bilayers
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10.1063/1.1862624
/content/aip/journal/jcp/122/12/10.1063/1.1862624
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/12/10.1063/1.1862624
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Illustration of the contours leading to the IK and H expressions for the local pressure tensor (open and filled arrows, respectively). The bold part of the IK contour indicates the fraction of the full virial from the interaction between and that is assigned to slab s according to Eq. (4). The bold part of the H contour indicates that the virial of the interaction from to is assigned to slab according to Eq. (6).

Image of FIG. 2.
FIG. 2.

Schematic illustration of the local pressure distribution coming from the IK and H expressions (solid and dotted lines, respectively) when varying the slab width. See text for details.

Image of FIG. 3.
FIG. 3.

Total pressure profiles from the IK and H expressions (four-point running average). Both are calculated with a cutoff of 20 Å for the electrostatic interactions. The coordinate is defined normal to the bilayer with origin in the bilayer center of mass. To indicate the dimension of the bilayer, the values corresponding to the maximal phosphorus density are marked with the letter on the top axis of the graph. The solid gray lines show the upper and lower standard deviations [SE(IK)] of the average IK profile.

Image of FIG. 4.
FIG. 4.

Five pressure profile contributions calculated by the H expression for the bonded, valence angle, dihedral, van der Waals, and electrostatic interactions in a DPPC lipid bilayer (four-point running average). The sum of these contributions gives the total H pressure profile in Fig. 3. The coordinate is defined normal to the bilayer with origin in the bilayer center of mass. To indicate the dimension of the bilayer, the values corresponding to the maximal phosphorus density are marked with the letter on the top axis of the graph.

Image of FIG. 5.
FIG. 5.

Total pressure profiles (four-point running average) calculated using cutoffs of 8, 12, 16, and 20 Å as well using HE method (Ewald). The maxima in the phosphorus density are marked with the letter on the top axis of the graph. The standard error for all the pressure profiles is of the same magnitude as the standard error for the IK profile in Fig. 3.

Image of FIG. 6.
FIG. 6.

The solid line is the lateral radial charge profile measured from aliphatic carbon atoms . The dotted line is the lateral radial charge profile measured from phosphorus atoms in the region . See text for details. As in the simulations, the electrostatic interactions between atoms that interact through covalent bonds or valence angle interactions were excluded in the calculation of the lateral charge profile.

Image of FIG. 7.
FIG. 7.

Partial charges for the DPPC lipids in the simulation. The atoms in the lipid “backbone” are drawn in gray. The atoms in the three methyl groups on nitrogen have identical charges but for clarity only one methyl group is shown explicitly. The solid zigzag line in the sn2 chain indicates that these atoms have been assigned new charges that are equal to the corresponding charges in the sn1 chain. For clarity, the atoms are only shown explicitly in the sn1 chain. The dashed lines in the sn1 and sn2 chains symbolize the rest of the acyl chain where the CHARMM27 charges were used. An over-bar indicates that the charge is negative.

Image of FIG. 8.
FIG. 8.

The area per lipid as a function of time. Note that there is no drift in the area per lipid and that the average area is . The data were obtained using a new lipid parameter set developed by the authors and co-workers.

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/content/aip/journal/jcp/122/12/10.1063/1.1862624
2005-03-25
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Methodological problems in pressure profile calculations for lipid bilayers
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/12/10.1063/1.1862624
10.1063/1.1862624
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