[gmx-users] zero temperature II
mbx0009 at yahoo.com
Sun Apr 4 15:33:01 CEST 2004
In a previous mail I mentioned a problem
with zero temperature output. I seem to have
found what the problem is and this looks like
a bug, or at least an undocumented limitation.
When I do md with a system containing only frozen atoms
and (not-frozen) water both ener.edr and md.log say
that the kinetic energy and the temperature are
zero. The thermostate seems to work though, because
my system does not "explode".
If I "un-freeze" the frozen atoms the
output is back to normal. The fact that frozen atoms
are formally provided with an infinite mass
might somehow cause this problem.
Any ideas for a work-around ?
Where in the code is E_kin calculated ?
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