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.
-----------------------------------------------------------
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= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
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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 Mon Dec 12 2011 - 17:00:02 PST
