On Sat, Jan 23, 2016, jinfeng liu 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.
> So, Can anyone help to explain why the calculated diffusion constant is
> much smaller than the experimental value ?
Be sure to check the papers that describe the SFC/fw model to make sure that
it is calibrated to obtain the experimental value. The tests you describe are
best used to compare the diffusion constant to the *calculated* values
reported in the literature.
...good luck...dac
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Received on Sat Jan 23 2016 - 07:30:03 PST
