Hi, 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? Thanks, Manik Mayur
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