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 coupling. Thank you. Barmak 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? Roland -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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