[gmx-users] Online Guide for MacOSX

Lee Cheng Siang lee at univ-montp2.fr
Mon Nov 17 11:44:01 CET 2003


I recently upgraded my PowerBook to Panther and installed X11 with the  
SDK package as well. I did an "archive and clean install" upgrade. Then  
I trashed my "Previous system" folder. Now I think Gromacs went down  
into the dustbin together with the "previous system" folder.

Everything seems to be a mess now with my iTerm not working properly  
and so many .*rc files flying about everywhere!!! They even change the  
standard shell from tcsh to bash...

So I wonder if anyone has seen a website trying to help people like me  
to re-animate my Gromacs+VMD+X11 combination which was working fine  
under Jaguar? Do I need to re-install fink+fftw+gromacs all over again?

I did a fink self-update, but when I run my commands from Terminal.app  
or iTerm.app or rxvt under X11, nothing happens! I need to go to  
/sw/bin to run the commands locally? I'm a SUPER totally confused right  
now. Any Gurus here to help me?

Thank you.

Le 17 nov. 03, à 09:07, David van der Spoel a écrit :

> By the way,
> a problem in drawing boxes is how to deduce which shape a
> non-rectangular box has. Given the box matrix one can deduce *for
> gromacs* whether it is a truncated octahedron, or rhombic dodecahedron.
> However, the coordinates are stored in the triclinic cell format,  
> unless
> they are converted back to the compact format (trjconv -ur compact).
> So given the box there are still two possibilities. As a user I'd like
> to make an animation of my protein in the dodecahedron, but to do that  
> I
> must back convert my trajectory. It seems therefore wise to let the  
> user
> choose the box rather than try to deduce it intelligently...
> Hope I make myself clear, the PBC stuff is quite well described in the
> GROMACS manual.
> --  
> David.
> _______________________________________________________________________ 
> _
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> +
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"Sans la liberté de blâmer, il n'est pas d'éloge flatteur" -  

Kenichi ZhenXiang LEE (Alex),
Université Montpellier 2,
34000 Montpellier, FRANCE.
Tel : 04 67 14 33 66 (laboratoire)
          06 61 43 72 27 (portable)

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