[gmx-users] Measure of density in homo- and heterogeneous systems

Justin A. Lemkul jalemkul at vt.edu
Mon May 28 21:11:27 CEST 2012

On 5/28/12 3:09 PM, James Starlight wrote:
> Dear Gromacs users!
> In this task I have two systems:
> First system consist of single layer of Ccl4 molecules.
> Second system consist of membrane-mimicking layer of Ccl4 surrounded by water
> and the protein embedded in that biphastic layer.
> I'd like to measure density in both of my systems to check of its packing
> degree. How could I do it in the case of homo system- (where I'd like to check
> density in the Ccl4 layer only) as well as in more complex hetero  system (
> where I'd like to check density in each layer separately as well as compute
> averaged density among all layers) ?

The density of the homogeneous system can easily be obtained from the .edr file, 
as long as the ensemble was NPT.  With NVT, the density term is not written, IIRC.

In the case of the heterogeneous system, use g_density to obtain partial 
densities as a function of box dimension.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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