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 <jalem...@vt.edu <mailto:jalem...@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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