Yes, I tried as much as possible to replicate his simulation in that paper.
But he ran the simulation using DL_POLY package, not Amber. So I am not
sure where the problem is. According to my knowledge, the Nose-Hoover
thermostat is used for the first time in AmberTools15, I don't know anyone
tested it before.
2016-01-23 19:35 GMT+08:00 <hannes.loeffler.stfc.ac.uk>:
> So I assume it is a simulated result then? If so what was his simulation
> setup/code that is have you tried to replicate his as much as possible?
> Anything special about the analysis of the results e.g. use of multiple
> time origins, etc.?
>
> ________________________________________
> From: jinfeng liu [jinfengliu1119.gmail.com]
> Sent: 23 January 2016 11:27
> To: AMBER Mailing List
> Subject: Re: [AMBER] Water diffusion constant obtained in Nose-Hoover
> thermostat in Amber14+AmberTools15
>
> The expected diffusion constant is 0.232, according to Gregory A. Voth's
> SPC/FW paper.
>
> 2016-01-23 19:23 GMT+08:00 <hannes.loeffler.stfc.ac.uk>:
>
> > 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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> >
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> >
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Received on Sat Jan 23 2016 - 04:00:05 PST
