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
Apologies for mis-reading your question.
You need to look at the definition of what radial distribution function
actually means and calculates, the atom density falls out of that.
What they are asking for is the atom density, p(r)local, as a function of
distance r from the center of the vesicle.
Dear Dr. Dallas Warren,
Many thanks for your response. I calculated the radial distribution function of
atoms on the surface of vesicles relative to the vesicle center of mass. I
submitted my paper and the referees asked me to calculate the radial density
profile instead of radial distribution
Hello Lalehan and Justin,
Thanks for the suggestion! The following patch :
https://gerrit.gromacs.org/c/gromacs/+/14542 does exactly that.
Best,
Christian
On 2019-11-29 14:23, Justin Lemkul wrote:
On 11/29/19 7:18 AM, Christian Blau wrote:
Hello Lalehan,
a.u. stands for "arbitrary
Thank you for your answer. As Mala said, since it is called the reference
structure, I was thinking that the RMSF was computed with respect to this
structure and not the average structure.
Is there any way with Gromacs to compute RMSF exactly with respect to a
given structure? If I want to study
Hello Justin, thank you for the response.
In that case I should use "frequency" if I plan to take it the way it is.
Thanks,
On Fri, Nov 29, 2019 at 4:25 PM Justin Lemkul wrote:
>
>
> On 11/29/19 7:18 AM, Christian Blau wrote:
> > Hello Lalehan,
> >
> >
> > a.u. stands for "arbitrary units".
>
On 11/29/19 7:18 AM, Christian Blau wrote:
Hello Lalehan,
a.u. stands for "arbitrary units".
The rmsd-dist contains a histogram over the distribution of rmsd
values, you can read the a.u. as counts per length-interval.
I would suggest that all histograms that GROMACS produces actually
On 11/29/19 5:53 AM, Mala L Radhakrishnan wrote:
Hi,
I am confused a bit by this answer -- isn't the file specified by -s used
for defining the rmsf (this is what is called the "reference" structure in
the documentation, and I have found that my results do vary using a
different "-s"
On 11/29/19 3:27 AM, Mijiddorj B wrote:
Dear Justin,
As you suggested, I generated the charmm36 parameter using cgenff for
single unit with two capping groups. After that, I created 3 residues based
on the parameter of cgenff including N-ter side, Middle, and C-ter side
residues. However,
The terminal selection should be NONE. First, you should have a CPN
structure with disulfide bonds.
https://www.tandfonline.com/doi/abs/10.1080/07391102.2019.1570341
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Hello Christian!
Thank you for the valuable information :)
Best,
Lalehan
On Fri, Nov 29, 2019 at 3:18 PM Christian Blau wrote:
> Hello Lalehan,
>
>
> a.u. stands for "arbitrary units".
>
> The rmsd-dist contains a histogram over the distribution of rmsd values,
> you can read the a.u. as
Hello Lalehan,
a.u. stands for "arbitrary units".
The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per
length-interval.
Best,
Christian
On 2019-11-29 12:57, Lalehan Ozalp wrote:
Hello everyone, I ran a cluster analysis for a 10 ns
Hello everyone, I ran a cluster analysis for a 10 ns simulation and
produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg file,
I see "a. u." in the y axis which I couldn't entirely understand. Is it
supposed to stand for atomic unit for length or mass or something else? I
provide
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
Hi,
I am confused a bit by this answer -- isn't the file specified by -s used
for defining the rmsf (this is what is called the "reference" structure in
the documentation, and I have found that my results do vary using a
different "-s" file)...? Or is that just used for fitting and then the
Hi,
On Fri, Nov 29, 2019 at 8:30 AM Sahil Lall wrote:
> Hello,
>
> Thank you for your suggestions, gave me some insight into my own work.
> However, the problem still persists.
>
> > With the option -ignh, you request pdb2gmx to add H atom. Thus, if you
> have already H atoms in the pdb I
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
Hi,
On Thu, Nov 28, 2019 at 1:23 PM Pragati Sharma
wrote:
> Hello users,
>
> I am trying to plot stress-strain curve for natural rubber from NPT
> simulations using the "deform" option. Deform along x direction at 1 bar
> pressure. The parameters I gave in mdp file are:
>
> Pcoupl
Dear Justin,
As you suggested, I generated the charmm36 parameter using cgenff for
single unit with two capping groups. After that, I created 3 residues based
on the parameter of cgenff including N-ter side, Middle, and C-ter side
residues. However, the net charges of these residues are not equal
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