[gmx-users] bilayer area questions WITH DATA

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Thu Sep 15 01:09:25 CEST 2005

Just to clarify the point ....

> 3) After 10 nanoseconds of equilbriation
> new system size :  7.368  8.177  8.785

This is the total distance, in the x, y and z directions, from the most
extreme atoms present "within" the simualtion box.  The atoms aren't
actually outside of the box though, they are present within the box on
the opposite side of the simulation box.  That is what the periodic
boundary condition does.  However, the molecules are kept whole, not
fragemented.  So when you load up the coordinate file it looks like that
atoms are stuck out into nothing.

> new center      :  2.881  2.936  4.316 (nm)
> new box vectors :  5.692  5.876  8.640 (nm)

This is the actual size or dimensions of the simulation box.  Multiply
these together and you will get the box volume.  Use the x and y values
to get the bilayer area.

> new box angles  :  90.00  90.00  90.00 (degrees)
> new box volume  : 288.95               (nm^3)

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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