On 2010-11-27 23.54, Apoorv Kalyankar wrote:
Hi,
I was wondering how does a thermostat work in a Non Equilibrium
Simulation(NEMD) in GROMACS.
Does it subtract out the streaming velocity before applying the
thermostat or does it not apply thermostat at all in
the direction of the applied acceleration?
Thanks.
check source code in src/mdlib/update.c
IIRC it does not scale the group velocities resulting from acceleration
and hence only the internal temperature is scaled.
Apoorv Kalyankar
Graduate Student
Mechanical Science and Engineering
Unviersity of Illinois at Urbana-Champaign
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Dept. of Cell & Molec. Biol., Uppsala University.
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