VMD-L Mailing List

From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Wed Mar 16 2011 - 14:33:58 CDT

Thanks a lot for the file.
I've started to learn TCL, but i'm still a beginner, and in this case i
really needed it as soon as possible. Couldn't wait until i had learned all
TCL. But you right, i had realized it sooner, that's why i bought a "bible"
of tcl programming.

Well, thanks again.

Ranyere Deyler Trindade

On Wed, Mar 16, 2011 at 4:23 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Mar 16, 2011 at 3:12 PM, Ranyere Deyler <ranyere_at_gmail.com> wrote:
> > Well, i just thought it was logical. But it seems not.
> > Does anyone have a script that calculates the MSD using VMD? I don't know
> > much about tcl to build one. If anyone knows about a script that does
> that i
>
> then you better start teaching yourself some tcl,
> if you are serious about using VMD for analysis.
> since most advanced analysis processes with VMD
> require customizations and you'll have to do testing
> of applicability for your purposes yourself.
>
> > would appreciate.
>
> i am attaching what i had written a while ago for
> a computational chemistry class. no warranties,
> and no support. it may eat up your computer.
>
> axel.
>
>
> > Thanks a lot.
> > Ranyere Deyler Trindade
> >
> > On Wed, Mar 16, 2011 at 12:54 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Wed, 2011-03-16 at 11:24 -0300, Ranyere Deyler wrote:
> >> > Dear VMD users, i searched in the list for this question and i saw one
> >> > or two reply but it's still not clear.
> >> >
> >> >
> >> > What i want is to plot the MSD over time, so i can plot it and get
> >> > some information over de diffusion, whether it is a superdiffusive or
> >> > subdiffusive proccess.
> >> >
> >> >
> >> > Well, namd has the "RMSD trajectory" plugin. So, theoretically i would
> >> > have to get the square of the RMSD found on VMD plugin and then plot
> >> > it.
> >> >
> >> >
> >> > So i ask. Is that right? In this case, of vmd plugin, the square of
> >> > the RMSD trajectory will give me the MSD?? Can i use it to look at the
> >> > diffusion coefficient??
> >>
> >> it is a _very_ bad idea to use acronyms as a base for science.
> >> the RMSD that the plugin computes is something different from
> >> the MSD that you compute for self-diffusion.
> >>
> >> axel.
> >>
> >> >
> >> > Thanks a lot.
> >> >
> >> >
> >> > Ranyere Deyler Trindade
> >>
> >> --
> >> Dr. Axel Kohlmeyer
> >> akohlmey_at_gmail.com http://goo.gl/1wk0
> >>
> >> Institute for Computational Molecular Science
> >> Temple University, Philadelphia PA, USA.
> >>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>