Hi,
Apologies for adding to a long list of comments, but I thought it might be worth mentioning since you seem to be trying to replicate (doi: 10.1063/1.2136877) which appears to have obtained its diffusion constants under NPT conditions.
I could be wrong (apologies if I am / if this has already been mentioned) but it seems that the self-diffusion constant is given as 0.23 in units of 10^-5 cm^2 / s rather than A^2 / ps .
As far as I am aware cpptraj's diffusion command reports its values in A^2/ps (manual page 562). From your original email it seems that your value of 0.15 is reported in A^2/ps? Converting this by 10/6 would give you 0.25 x 10^-5 cm^2 / s which is much closer to what is reported in the literature.
Best regards,
Irfan Alibay
PhD Student
Pharmacy School
The University of Manchester
________________________________________
From: jinfeng liu [jinfengliu1119.gmail.com]
Sent: Saturday, January 23, 2016 11:27 AM
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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Received on Sat Jan 23 2016 - 14:30:03 PST
