Hi,
I am studying the dynamics of a double stranded DNA in presence of
small molecules. I want to study the preferential binding of these
molecules in the grooves and backbones of the DNA and also calculate the
feasibility of these binding in terms of calculating the free energy
change.My quest
Dear all,
I have a curved rod-like micelle formed by three different molecules. I
want to calculate the RDF of constituent molecules. I want to select the
center line of the curved cylindir-like structure as a reference point. How
can I do that? I am using Gromacs version 5.1.2. with Martini Force
Dear gmx-users,
I am new to Gromacs. I have a droplet including some types of lipids such
as DPPC. I want to calculate RDF for head atom of DPPC with respect to
droplet center-of-mass. My question is how can i calculate this issue in
versions 2017. Apparently this feature has been removed from cur
Well, since you are not interested in the duplex stability, I would not use
-COM. See, during the simulation, the center-of-mass of such a small helix
part can drastically move, leading to a questionable result. Check your
system and make sure that you will not face this situation.
About the PMF,
On 12/27/14 4:17 AM, soumadwip ghosh wrote:
Hi,
I am studying the dynamics of a double stranded DNA in presence of
small molecules. I want to study the preferential binding of these
molecules in the grooves and backbones of the DNA and also calculate the
feasibility of these binding in ter
Dear all,
I am working on a wormlike micelle that has a curved structure. I want to
calculate the radial distribution functions of constituent molecules with
respect to the backbone (the line following the micelle length and
represents the center of the curved cylindrical structure) of the wormlik
See here for info on the selection syntax
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
On Wed, Mar 14, 2018 at 10:01 AM, Esra Kaçar wrote:
> Dear all,
>
> I am working on a wormlike micelle that has a curved structure. I want to
> calculate the radial distribution funct
Dear Joe,
Sorry for the confusion. I am working with martini force field and I have
three different molecules in the micelle structure. I want to analyze the
RDF of the constituent molecules with respect to the line that pass through
the center along with its length. As I mention before this line
You cannot use a line as the reference. From a brief glance at the paper
you link it seems like maybe you actually want to compute the expectation
value of the micelle backbone, a method known as principle curves which is
a generalization of principle component analysis. At any rate, you should
pro
@maillist.sys.kth.se
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >1. rdf calculation for wormlike micel
Hi all,
I am trying to calculate the RDF between the protein surface and the centre of
mass of my ligand and water molecules. Please find below the command I used:
gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin 0.02
-cn number.xvg -surf mol -seltype mol_com
I get the
-surf flag is used with -ref flag. Provide the reference file in the -ref
flag.
On Thu, Feb 6, 2020 at 1:52 AM Pandya, Akash
wrote:
> Hi all,
>
> I am trying to calculate the RDF between the protein surface and the
> centre of mass of my ligand and water molecules. Please find below the
> comman
Dear gmx-users,
The radial distribution function with respect to center-of-mass was computable
in old gromacs versions. How can I calculate that in newer version(2016)?
Thanks in advance.
Maryam
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Dear gmx-users,
The radial distribution function with respect to center-of-mass was computable
in old gromacs versions. How can I calculate that in newer version(5.1..)?
Thanks in advance.
Maryam
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