Adrien Leygue wrote:
Dear Gromacs users,
I am experiencing several problems which all seem to relate to single
vs. double precision.
1-) I am doing simulations of a liquid crystal system using a custom
force field but whenever I try to run them in parallel they all crash
after some time (238 ps) unless I run them in single precision. The
error message tend to vary but it is usually something like:
please run tpbconv_d -f -s -e -time 230 -o test.tpr
test whether this tpr crashes in double but not in single, and if it
still crashes please submit a bugzilla.
Have you done make distclean between compilations?
2-) I am also doing simulations of coarse grained molecules using
virtual sites and home-made tabulated potentials (using several
table_X_Y.xvg files). I haven't tried parallel runs. These simulations
run prefectly in double precision but whenerver I try to go to single
precision they crash almost immediately (prior energy minimization is
performed in double precision). I have tried to re-run some energy
minimization on the system in single precision but this stops
immediately as well. Looking at the output I see huge forces and
potential energy which are not present in double precision. However if
I remove all non-bonded interactions (I do not have charges) in the
topology file the energy minimization works fine in single precision.
I can however simulate a LJ fluid using any of the above tabulated
potential. I assume there must be some coupling between constraints,
virtual sites, and tabulated potentials but then why does it work in
single precision.
The spacing in single precision tables is usually different than in
double, but this should be taken care of automatically.
Again if you have a tpr that crashes in single but not in double then
you are welcome to submit a bugzilla.
I welcome any help or suggestion on how to investigate these issues. I
haven't attached any file (mdp, topology,...) but I can send them.
Thanks a lot for your help.
Adrien.
--
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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