Bert wrote:
Dear gmx-users,
I have done a test using test suit 4.0.4, and I got some failures as follows.
All 16 simple tests PASSED
FAILED. Check files in aminoacids
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
4 out of 14 complex tests FAILED
Check the files in these directories to see if the differences are acceptable,
as explained on the wiki:
http://wiki.gromacs.org/index.php/Test-Set
<snip>
16 out of 63 kernel tests FAILED
These failures are a known issue and a bugzilla has been filed. They affect
Buckingham interactions.
All 45 pdb2gmx tests PASSED
My gcc version is 4.1.1, and both gmx 4.0.4 and 4.0.5 get exactly the
same failures on my Xeon 8 core based linux. For example, in
/kernel/kernel020
As warned on the Gromacs site: "WARNING: do not use the gcc 4.1.x set of
compilers. They are broken. These compilers come with recent Linux distrubutions
like Fedora 5/6 etc."
Users have reported non-functional or improperly-functioning executables
produced by the 4.1.x series.
-Justin
checkpot.out gives:
--------------------------------------------------------------------------
comparing energy file reference_s.edr and ener.edr
There are 39 terms in the energy files
There are 12 terms to compare in the energy files
LJ-14 step 0: -63.1209, step 0: 6.50742
Potential step 0: -321.601, step 0: -251.972
Files read succesfully
--------------------------------------------------------------------------
checkvir.out gives:
--------------------------------------------------------------------------
comparing energy file reference_s.edr and ener.edr
There are 39 terms in the energy files
There are 25 terms to compare in the energy files
LJ-14 step 0: -63.1209, step 0: 6.50742
Potential step 0: -321.601, step 0: -251.972
Kinetic En. step 0: 15.0135, step 0: 29.0739
Total Energy step 0: -306.588, step 0: -222.898
Temperature step 0: 1.93226, step 0: 3.74185
Pressure (bar) step 0: -3095.37, step 0: -2497.79
Vir-XX step 0: 1127.45, step 0: 1075.85
Vir-XY step 0: 63.524, step 0: 21.7761
Vir-XZ step 0: -264.813, step 0: -260.354
Vir-YX step 0: 63.5241, step 0: 21.777
Vir-YY step 0: 803.252, step 0: 581.702
Vir-ZX step 0: -264.813, step 0: -260.354
Vir-ZZ step 0: 321.207, step 0: 176.573
Files read succesfully
----------------------------------------------------------------------------
The deviations are obvious. Any suggestion would be appreciate. Thank you.
Best Regards,
Bert
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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