Justin A. Lemkul wrote:
Quoting David van der Spoel <[EMAIL PROTECTED]>:
Justin A. Lemkul wrote:
Hi All,
I recently installed Gromacs version 3.3.3 on a dual-core Intel MacBook
running
OS X 10.5.2 (Leopard). The default gcc from XCode was 4.0.1, and the
Gromacs
installation went just fine (serial and parallel) when using this gcc. I
know
that the download site mentions that gcc 4.1.x is broken, and the problems
with such compilers have been well-documented across this list, but I was
wondering if anyone know if gcc 4.0.1 was problematic as well. I had no
problems during any phase of the installation, but I just wasn't sure if
I'd
develop some strange error using an analysis tool.
I can also install gcc-3.3 in another location, and can easily make that
the
default gcc, but I was just curious to see if 4.0.1 was alright to avoid
the
effort, if possible :)
I think it is fine, but you can run the test set to be ( a bit more ) sure.
Thanks David. I ran the test set, and got the following:
$ ./gmxtest.pl all
No topol.tpr file in morse. grompp failed
FAILED. Check files in morse
1 out of 16 simple tests FAILED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
Error not all 45 pdb2gmx tests have been done successfully
Only 38 energies in the log file
For the "No topol.tpr file in morse" error, the grompp.out file shows:
Fatal error:
number of coordinates in coordinate file (conf.gro, 1490)
does not match topology (topol.top, 0)
...although I'm not sure why.
Look further up in the grompp.out file
The dec+water failure has been discussed before, although the discrepancy is
slightly different than that listed on the wiki:
There are 5 terms to compare in the energy files
LJ (SR) step 34: -0.21167, step 34: -0.171631
The pdb2gmx.log file shows that there is some discrepancy in the .mdp
parameters:
WARNING 1 [file ../../../../em.mdp, line unknown]:
Unknown left-hand 'bd-temp' in parameter file
checking input for internal consistency...
processing coordinates...
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: futil.c, line: 345
File input/output error:
b4em.gro
-------------------------------------------------------
I'm guessing this is just a reflection of changes that have been made between
versions 3.3.2 and 3.3.3? But I don't know what to make of the "38 energies in
log file." Is there some more relevant output I can post to help clarify the
situation?
Again, here you may need to look more closely in the output file. If
b4em.gro does not exist something went wrong before.
Thanks,
Justin
Thanks for any insights.
-Justin
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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