[gmx-users] g_energy and pressure values

David van der Spoel spoel at xray.bmc.uu.se
Thu May 2 19:43:00 CEST 2002

On Thu, 2 May 2002, McMullen, Roger  L wrote:

>I have a fatty acid monolayer (64 fatty acids) on H2O with a packing density
>of 20 A^2/molecule.  We are trying to simulate a Langmuir trough experiment
>in which lateral pressure is monitored as a function of the molecular
>packing density (perimeter area).  As a first approximation, we would like
>to keep the volume of the box constant in order to maintain a packing
>density of 20 A^2/molecule and monitor the corresponding lateral pressure.
>We have run the simulations and are trying to use g_energy to calculated the
>pressure.  g_energy provides various pressures: Pres-XX, Pres-XY, Pres-XZ,
>Pres-YX, Pres-YY, Pres-YZ, Pres-ZX, Pres-ZY, and Pres-ZZ.  What do these
>pressures correspond to?  Does any one have any experience working with such
>a system?
The pressure is a tensor (see manual for definition). For your work you
probably only need the diagonal elements, but you will find that the
off-diagonal is small on average and symmetric.

Check older work by Van Buuren and Berendsen
  author =	 "A. R. van Buuren and H. J. C. Berendsen",
  title =	 "Molecular dynamics simulations of carbohydrate based
                  surfactants in surfactant/water/oil systems",
  journal =	 "Langmuir",
  year =	 "1994",
  volume =	 "10",
  pages =	 "1703--1713",
  author =	 "Aldert R. van Buuren and Jacob de Vlieg and Herman
                  J. C. Berendsen",
  title =	 "Structural Properties of 1,2-Diacyl-{\em
                  sn}-glycerol in Bulk and at the Water Interface by
                  Molecular Dynamics",
  journal =	 "Langmuir",
  year =	 "1995",
  volume =	 "11",
  pages =	 "2957--2965",

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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