[gmx-users] Online Guide for MacOSX

[Erik Lindahl]

Hi Lee,

I did a clean install of Panther, so I can't help you with the details,  
but:

1. I used the source distribution of fink-0.6.0. Works great, but it  
takes a while to install since it has to compile everything.

2. There is nothing in Gromacs that forces a recompile of FFTW, but  
since the compilers have changed (gcc-3.3 now) and there might be some  
new system libraries I would still recommend to do it.

3. gcc-3.3 issues some new warnings - you can use the recent  
gromacs-3.1.5_pre2 source distribution from ftp.gromacs.org/pub/beta to  
get rid of these.

Cheers,

Erik


On Nov 17, 2003, at 2:44 AM, Lee Cheng Siang wrote:

> Hello,
>
> 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" -  
> Beaumarchais.
>
> Kenichi ZhenXiang LEE (Alex),
> LEMP-MAO,
> Université Montpellier 2,
> 34000 Montpellier, FRANCE.
> Tel : 04 67 14 33 66 (laboratoire)
>          06 61 43 72 27 (portable)
>
>
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