On Sat, Jan 23, 2016, David Case wrote:
> >
> > I performed liquid water dynamics using the latest
> > Amber14+AmberTools15. I used the SPC/fw water model in Nose-Hoover
> > thermostat (I found this thermostat in the latest Amber manual). But, the
> > water diffusion constant calculated in 1 ns MD simulation was 0.15,
> > comparing to the experimental value of 0.23 A^2/ps.
>
> Using thermostats and barostats changes Newton's equations of motion, and
> will invalidate attempts to understand time-dependent behavior. After
> equilibration at the desired temperature and pressure, you will need to run
> an NVE simulation, and analyze that to get dynamics.
Just an additional note: be sure to check energy conservation carefully. With
flexible waters, you may need to use a pretty short time step, such as 0.5 fs.
....dac
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Received on Sat Jan 23 2016 - 13:00:04 PST
