[gmx-users] Thermostating in NEMD

David van der Spoel spoel at xray.bmc.uu.se
Sun Nov 28 11:16:11 CET 2010

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

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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