[gmx-users] COMM removal and thermostat

Manik Mayur manik.mayur at gmail.com
Tue Dec 9 19:41:59 CET 2008

I have just ventured into this wonderful world of molecular dynamics and am
learing and using GROMACS to validate some papers as a learning exercise. I
have a nanopore system in which a wall has 3 layers and the molecules are
tethered by a spring. I am doing COMM removal for each layer with a
frequency of step 1 and have applied a berendsen thermostat to it.
Since GROMACS adjusts the COMM by removing the COM momentum(velocity) from
the system, and for thermostat, a similar thing is done(KE/velocity
adjustment) from each molecule. I wonder should there be any relation
between the step size of COMM removal and Tau_t of the thermostat?
Manik Mayur

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