[gmx-users] diverging temperature with pressure coupling

Roland Schulz roland at utk.edu
Sun Apr 17 09:10:21 CEST 2011

Forwarding this email from my group colleague:

Dear Gromacs users,

I am trying to simulate a cellulose fiber in an ionic liquid solution in the
NPT ensemble.  During the simulation, the entire system is coupled to a
thermostat.  Yet, I observe an inhomogeneous temperature distribution
throughout my system (hot-solvent/cold-solute) when I use Parrinello-Rahman
pressure coupling but NOT when I employ Berendsen pressure coupling.  I have
tested velocity-rescaling and the Nose-Hoover scheme to keep the temperature
constant and in both cases Parrinello-Rahman pressure coupling seems to
cause the solute’s temperature to become significantly lower than the
solvent’s (to decompose temperatures, I am using “mdrun -rerun” with a run
input that defines tc_grps separately).

I was wondering whether there were any known algorithmic reasons for this
unphysical temperature gradient when using Parrinello-Rahman pressure

Thank you.


Comment from me: The effect is large. The ionic liquid is 5 degrees higher
and the cellulose is 50 degrees lower (after 50ps, after that it stays
constant). With Berendsen pressure both parts fluctuate around the same
target temperature (as one would expect). Any reason why one doesn't get the
correct temperature with rerun? Or is their a better way to get the
temperature for different groups(for a simulation with just one tc-group)?
Any reason why Parrinello-Rahman pressure coupling would have this effect on
the temperature?


ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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