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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