[gmx-users] Online Guide for MacOSX
lindahl at csb.stanford.edu
Mon Nov 17 18:22:00 CET 2003
I did a clean install of Panther, so I can't help you with the details,
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.
On Nov 17, 2003, at 2:44 AM, Lee Cheng Siang wrote:
> 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
> 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
>> However, the coordinates are stored in the triclinic cell format,
>> 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
>> 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
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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)
> gmx-users mailing list
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