Hi Ilyas and Tom,
I'm installing AMBER11 in order to access the raw format, which wasn't
available in AMBER9.
I'll check out GNUPlot and Mathematica. I think the 2D plot is very
useful; I'm surprised it isn't used more often.
Thanks so much for your help!
-Dave
On Mon, Dec 12, 2011 at 7:35 PM, Ilyas Yildirim <i-yildirim.northwestern.edu
> wrote:
> If you have Mathematica, you can use that program to make 2D contour
> plots. Mathematica has a lot of nice options in it.
>
> Ilyas Yildirim, Ph.D.
> -----------------------------------------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = http://www.pas.rochester.edu/~yildirim/ =
> -----------------------------------------------------------
>
>
> On Mon, 12 Dec 2011, David Condon wrote:
>
> > Hello all,
> >
> > is anyone aware of how to add/label axes in a 2D RMS plot? It seems like
> > this command has fallen out of favor lately, but I find it very useful.
> >
> > For some reason this section was omitted from the AMBER9 manual.
> >
> > The input I'm using is:
> >
> > trajin mdall.mdcrd 1 20000 10
> >>
> > 2drms out 2drms.ps ps mass :1-4 time 1.0
> >>
> >
> > Unfortunately, the axes aren't labeled in the post-script file like they
> > are with the more commonly used "rms" command.
> >
> > Also, the numbers in the file:
> >
> > 0.8307 fillbox
> >> 1.2500 inch 1.3970 inch box
> >> 0.9114 fillbox
> >> 1.2500 inch 1.4000 inch box
> >> 0.7119 fillbox
> >> 1.2500 inch 1.4030 inch box
> >> 0.6622 fillbox
> >> 1.2500 inch 1.4060 inch box
> >> 0.6858 fillbox
> >> 1.2500 inch 1.4090 inch box
> >> 0.7613 fillbox
> >> 1.2500 inch 1.4120 inch box
> >> 0.6574 fillbox
> >> 1.2500 inch 1.4150 inch box
> >> 0.6513 fillbox
> >> 1.2500 inch 1.4180 inch box
> >>
> >
> > don't appear to match the RMSD, which should be around 6 Angstroms. What
> > do these numbers mean?
> >
> > your response is greatly appreciated!
> > -Dave
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> >
>
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Received on Tue Dec 13 2011 - 08:00:03 PST
