[gmx-users] Online Guide for MacOSX

[Kay Gottschalk]

Hi Erik,

did you try g_rdf? For some reason it doesn't work for me and gives  
segmentation fault. I have no idea what the reason is (I us 3.5.1_pre2)  
- perhaps I did some error in the installation, or my .cshrc is wrong.  
Help would be appreciated. Everything else seems to work. Which  
compiler flags did you use? Did you try this -fast flag? Somehow it  
didn't work for me. Doing nothing with the flags worked (except for  
g_rdf...).
Cheers,
Kay.

On Nov 17, 2003, at 7:21 PM, Erik Lindahl wrote:

> 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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>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Rehovot
Israel