Have you looked into the literature to see what the expected diffusion behaviour of the water _model_ you use is?
________________________________________
From: jinfeng liu [jinfengliu1119.gmail.com]
Sent: 23 January 2016 11:10
To: AMBER Mailing List
Subject: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15
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
following:
&cntrl
imin=0,irest=1,ntx=5,
dt=0.001,nstlim=1000000,
ntb=2,ntp=1,taup=2.0,
igb=0, cut=8.0, jfastw=4,
ntt=9,gamma_ln=10.0,nkija=1,temp0=300.0,
ntpr=200,ntwr=200,ntwx=200,
&end
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 - 03:30:07 PST
