Date: Mon Feb 13 2012 - 09:21:33 CST
Dear NAMD users,
Lately in the lab we have been discussing about which thermostat use in our simulations. I know this can be just a detail, but it is quite tricky. The velocity rescaling method will not give he correct ensemble, but the langevin dynamics will affect the dynamics of the system and in principle quantities such as diffusion constants will be modified. For NVT simulations the Lowe-Andersen thermostat should be the option to avoid that, but we are doing NPT and the Langevin barostat already modifies the dynamics (it contains a "thermostat on its own right?).
Besides, as far as i remember the TIP3 water model (the one we are using) already has a higher diffusion constant and the langevin damping coefficient is used to somehow match it to the experimental value, so i do not know if it is possible to obtain the "correct" dynamics with TIP3 water and any “Galilean invariant” thermostat.
Does anyone have any insights on this topic?
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