[gmx-users] gmxtest, error during pdb2gmx step.

SeungPyo Hong sp1020 at gmail.com
Tue Apr 29 08:13:59 CEST 2008

Dear gmx-users,

Recently I installed Gromacs to a new cluster, SUN X4100, Dual Core AMD
Opteron (tm) Processor.
However during the test step, errors occur.
The following is the entire output of the "*$./gmxtest.pl -double all*"

    All 16 simple tests PASSED
    All 14 complex tests PASSED
    All 63 kernel tests PASSED
    N      Reference   This test
      10    -39.0984    -32.5043
      11    -39.0984    -32.5043
      12    -93.8123    -75.8897
      13    -93.8123    -75.8897
      21    -11007.5    -9915.17
    There were 5 differences in final energy with the reference file
    All 45 pdb2gmx tests PASSED
    pdb2gmx tests *FAILED*

I guess this seems to be a comparison between the precalculated
value(Reference) and the value calculated in my machine(This test).

That what is the probable causes of this problem?
I compiled the program again twice,  with *gnu compilers*, gcc.
Also the double precision fftw3 library is used.
Only the installing directory and the fftw3 library directories are given
during configuration.

Additionally, if I use 'xleap' of Amber package and using 'amb2gmx.pl'
script instead of 'pdb2gmx' program, is it OK?
(By doing this I use Amber force field in Gromacs.)
Anyhow, the programs seems to work without out making any troubles, but I
don't know whether I am wasting CPU time or not. ^^

Thank you ~

'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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