Hi Jinfeng,
The difference you see (which I don't think is huge) is most likely due to
an imperfect translation of the MD input from DL POLy to Amber. Diffusion
properties of water are very sensitive to many input parameters (as Hannes
indicated). The best discussion of this was published here:
http://pubs.acs.org/doi/abs/10.1021/ct400109a
-Christina
On Saturday, January 23, 2016, <hannes.loeffler.stfc.ac.uk> wrote:
> I'm afraid I can't answer this either. I was just wondering how sensitive
> the diffusion constant would be to statistics.
>
> Other points to consider: is the constant sensitive to the pressure
> algorithm that is if you use, say, the MC barostat would you have to expect
> (very) different results? The MSD computation should be pretty
> straightforward but any chance of a wrong conversion factor? You could
> counter-check to compute the MSD via the velocity autocorrelation function.
>
> ________________________________________
> From: jinfeng liu [jinfengliu1119.gmail.com <javascript:;>]
> Sent: 23 January 2016 11:49
> To: AMBER Mailing List
> Subject: Re: [AMBER] Water diffusion constant obtained in Nose-Hoover
> thermostat in Amber14+AmberTools15
>
> 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 <javascript:;>>:
>
> > 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 <javascript:;>]
> > 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 <javascript:;>>:
> >
> > > 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 <javascript:;>]
> > > 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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--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
http://home.chpc.utah.edu/~cheatham/
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Received on Sat Jan 23 2016 - 06:00:04 PST
