Hi,
i observed the following problem. if i simulate water (spc or tip4p)
with gromacs 4.0.5 i get with v-rescale or berendsen thermostat the
wrong temperature (ref_t = 300K -> average around 425K, in about 1-2ps),
but only in serial, not in parallel runs.
non-water molecules or nose-hoover thermostat make no problems.
see also http://lists.gromacs.org/pipermail/gmx-users/2010-March/049248.html
for mdp and log file.
gromacs was compiled with the following comands:
and in the file 'configure' all '-lmkl' were deleted (don't ask me why,
i don't really understand that stuff, the command were from our previous
phd student).
./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5"
make
make install
make clean
./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
-lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
-lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
--prefix="/share/apps/gromacs/4.0.5" --enable-mpi --disable-nice
--program-suffix=_mpi
make mdrun
make install-mdrun
for gromacs 4.0.5 i used the icc 9.1.046 compiler.
i also tried gromacs 4.0.7 with icc 9.1.046 and icc 10.1.008 with spc
water, v-rescale thermostat.
-> serial: too high temperature 425K iso 300K
-> parallel: no problems
with non-water (mesitylene) i have no problem in serial.
the problem does not come from grompp because i can use same tpr-file
for serial and parallel runs with the above results.
if someone needs more informations about this please tell me.
greetings
thomas
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