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

[Mark Abraham]

On 29/05/2012 3:21 PM, James Starlight wrote:
> Justin,
>
> the main problem is the my simulation in nvt ensemble :) I understand 
> that density is constant in that conditions but I'd like to find way 
> to check this values for different components of my system.

AFAIK, there's no easy way to do that with GROMACS tools. The problem 
lies in defining the shape over which you want to compute such a partial 
density, since you need to compute its volume. Any solution is likely to 
be at least a bit crude, even for a trivial case of a membrane-mimic in 
water whose interfaces are roughly orthogonal to a box vector.

g_select may be useful in forming a suitable subset, and g_sas may be 
suitable for computing density and/or volume.

Mark

>
>
> James
>
> 2012/5/28 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
>
>
>     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
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul, Ph.D.
>     Research Scientist
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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