[gmx-users] protein water rdf with coordination number

[Dallas Warren]

RDF ->
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html

Coordination number ->
https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions
Will need to integrate the g(r) with radius, using the particle
average density across the box.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Fri, 17 May 2019 at 17:56, Omkar Singh <omkantnirala92 at gmail.com> wrote:
>
> I have protein MD simulation file I want to find out protein water rdf with
> coordination number. Can anyone help regarding this?
>
> Thanks
>
>
> On Thu, May 16, 2019, 10:55 <battistia at libero.it> wrote:
>
> >
> > Dear gromacs members,
> >
> > I would ask you if in gromacs is possible to add a control parameter on
> > the Lennard-Jones interactions.
> > For example we have two atoms A and B and the corresponding parameters;
> > sigma(A), eps(A),  sigma(B), esp(B); then for the A-B interactions we have
> > the parameters obtained with the Lorentz-Berthelot or with the geometrical
> > average.
> >
> > I would like to have a standard interaction between A or B with the other
> > atoms of the system.  In the same time I would like to add a control
> > parameter C on the interaction between A and B to have the following
> > potential:
> > V(r(AB))=4*eps(AB)*[(sigma(AB)/r(AB))^(12)-C*(sigma(AB)/r(AB))^(6)]
> >
> > Is it possible? How can I manage this calculation?
> >
> >
> > Many thanks,
> >
> >
> > Anna
> >
> >
> >
> >
> > --
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