[AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15

From: jinfeng liu <jinfengliu1119.gmail.com>
Date: Sat, 23 Jan 2016 19:10:34 +0800

Dear Amber users,

        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. My MD input is like the

 igb=0, cut=8.0, jfastw=4,

The trajin file calculating the diffusion constant is like:

trajin md.crd
diffusion 0.2 :WAT.O average

According to the MSD calculated above, I obtained the diffusion value.

So, Can anyone help to explain why the calculated diffusion constant is
much smaller than the experimental value ?
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Received on Sat Jan 23 2016 - 03:30:06 PST
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