Hi all.
I am trying to perform a tpi (test particle insertion) calculation on a
trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf
cluster of Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz). I am using
tpi integrator in the mdp file and the following command:
$ grompp -f tpi.mdp -c 32hoa_128dmpcwrun.gro -n index_tpi.ndx -p
topol_tpi.top
$ mdrun -rerun 32hoa_128dmpcwrun.trr -g tpi.log
I tried different versions of gromcas and for 4.0.X I got a segmentation
fault getting the message:
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000 Segmentation fault
using a compiled version with "config --prefix
/home/cerezo/Programs/gromacs4.07" + "make" + "make install". However,
it works when I used a precompiled version (got with apt-get, I have
kubuntu). So I guess that it may be due to a mistake during the
compilation. In addition, other integrators (i.e. md, steep) work
correctly with the version I've compiled. My system is and Intel(R)
Core(TM)2 Quad CPU Q8400 @ 2.66GHz. Is there any trick I could try
in the compilation?
I also tried gromacs-4.5-betaX and it works but sometimes (apparently
randomly) the calculation gets stops (as if it had entered in an
infinite loop) after reading the last frame.
Thanks for your attention!
Javier
--
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
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