Hi Elham,
In general to calculate the radial density profile of a droplet-like
object one should do binning (histogram) in spherical coordinate along
radius. That means you should define a series of shell each with thickness
of dr and all centered on center of the vesicle. And then you could
You want to calculate the RDF between the center of mass of an appropriate
group that will be at the center of the vesicle (probably the surfactant,
or alkane chain of the surfactant, and need to ensure that you only have a
single vesicle that perform the calculation on) to the center of mass of
Dear all, I am working on vesicle structure of surfactants in water. I want to
calculate the radial density profile of surfactant headgroup atoms versus r.
The head group atoms are located on the vesicle surface.How can I plot the
radial density profile of headgroup atoms from the center of
The manual for version 4.6 is available online. The analysis command you
want is g_rdf, for version 4.6. g_rdf plots the radial distribution
function, which is what I think you are calling radial distribution curve.
The manual has a nice explanation of it so please check it out. The radial
density
Dear Gromacs Users,
I am working on a water- double walled carbon nanotube system. After the
completion of simulation using Gromacs 4.6.5, it was found that the water
molecules are present inside the double walled carbon nanotube as well as in
the bulk of the system. I want to plot the radial
Hi,
Am wondering how you can have an 'axis' for single stranded DNA
simulation? ssDNA should collapse quickly if starting from helical type
configuration unless you are considering only one strand from ds-DNA or
some restraints or very small ss fragment. If you are using RDF then I
assume your
Hi all,
I am looking for a way to calculate the radial density distribution
of ions surrounding A single stranded DNA axis. Is there a way to calculate
it using g_rdf or some other tool?
I am thinking of taking the g(r) profile and divide it by the volume
element 2*pi*r*h*dr ( where r is
Dear gromacs users
I would like to compute the radial density profile (1/nm-3) of
different parts of a micelle formed with SDS molecules (such as headgroup,
alkyl tail and water) relative to the center of mass of the micelle.
Is there a direct tool in gromacs to obtain this parameter? If not,
On 8/19/14, 8:46 AM, Atila Petrosian wrote:
Dear gromacs users
I would like to compute the radial density profile (1/nm-3) of
different parts of a micelle formed with SDS molecules (such as headgroup,
alkyl tail and water) relative to the center of mass of the micelle.
Is there a direct
Dear Justin
Thanks for your quick answer.
I want to obtain *radial density profile* relative to COM and not radial
distribution function (RDF) relative to COM.
Are you sure g_rdf -com is appropriate for this aim?
Thanks
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On 8/19/14, 9:02 AM, Atila Petrosian wrote:
Dear Justin
Thanks for your quick answer.
I want to obtain *radial density profile* relative to COM and not radial
distribution function (RDF) relative to COM.
Are you sure g_rdf -com is appropriate for this aim?
Sorry, misread. gmx density
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