[gmx-users] Online Guide for MacOSX

Mon Nov 17 18:53:01 CET 2003

On Mon, 2003-11-17 at 18:30, Kay Gottschalk wrote:
> 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,


a simple trick is to go to 
cd src/tools
rm g_rdf.o
gmake CFLAGS=-g install

> 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
> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> >>> +++
> >>>
> >>> _______________________________________________
> >>> gmx-users mailing list
> >>> gmx-users at gromacs.org
> >>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>> Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-request at gromacs.org.
> >>>
> >>>
> >> ********************************************************************** 
> >> *******
> >>
> >> "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)
> >>
> >>
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the
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> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> > interface or send it to gmx-users-request at gromacs.org.
> >
> >
> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
> Rehovot
> Israel
> 
> _______________________________________________
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-- 
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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