Hi Carlos and Jason,
I have visualized the periodic images, and the protein does not appear to be interacting with itself.
I have a question about the rdf. The rdf that I has structure, but the peaks are not well defined. Furthermore, the asymptotic value as the distance approaches the bulk is 0.9, not 1.0.
I have used the command
radial rad.dat 0.1 10.0 :WAT.O :ALA
radial rad2.dat 0.1 10.0 :WAT.H1 :ALA
radial rad3.dat 0.1 10.0 :WAT.H2 :ALA
The polypeptide consists of 20 alanine residues, and it is not spherical.
Thanks!
Krisitn
________________________________________
From: Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: Friday, February 05, 2016 1:42 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Size of solvent box, RDF
just to add a bit to Jason's response on VMD, this is turned on by checking
the boxes under the "periodic" tab in the representations window. this
works pretty well.
On Fri, Feb 5, 2016 at 1:36 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Feb 5, 2016 at 12:44 PM, Krantzman, Kristin D <KrantzmanK.cofc.edu
> >
> wrote:
>
> > Hi Carlos,
> > Thank you for responding.
> > I know this seems like a silly question, but how can I tell whether the
> > protein interacts with its periodic images?
> >
>
> Look at an imaged snapshot where the protein is at the center of the unit
> cell. Is the protein close to the edge of the unit cell in any of the
> dimensions?
>
> With VMD, you can also visualize multiple unit cells (in the
> representations pane). Then you can see quite clearly how close two
> periodic images are to one another and whether their dynamics seems to
> indicate they are interacting. (Basically what you're looking for are
> correlated motions on opposite sides of the protein that appear to arise
> through inter-image interactions.)
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Feb 05 2016 - 15:00:03 PST
