[gmx-users] Online Guide for MacOSX
kay.gottschalk at weizmann.ac.il
Mon Nov 17 18:31:01 CET 2003
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
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.
> 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
>>> 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
>>> 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
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>>> www interface or send it to gmx-users-request at gromacs.org.
>> "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
>> gmx-users at gromacs.org
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
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