# [gmx-users] Diffusion Coefficient from VAC

Thu Feb 23 16:14:43 CET 2006

```Hi,
There will be some difference between the value of D calculated from MSD and
VACF. I think your procedure is right. You can output it every 200fs if you
are doing it by MSD.
But do few things, in calculating MSD, do it in bins, like first calculate
the diffusion coefficient from MSD using 200-500 ps of the curve, then split
it into bins, 200-300ps, 300-400ps, and so on, and finally see whether they
are same or not.
About VACF, all you need is atmost 1ps of the curve("generally" speaking),
and you said you are outputting it every 1fs. so, Thats fine!
Go through this journal, which gives field dependence of diffusion
coefficient. You are doing it right, as you need a static diffusion
coefficient value, (so you can ignore cosine and things). "Analysis of the
velocity autocorrelation function of water" Balucani, U. et. al.
Thanks,

On 2/23/06, Alexandre Suman de Araujo <asaraujo at if.sc.usp.br> wrote:
>
> Ok, maybe I was not so clear.
>
> My system is constituted by only one ion and water molecules (1400). I´m
> trying to calculate de diffusion coefficient of this ion in water.
>
> Using MSD the value is in relative good agreement with experiment (MSD =
> 1.5x10^-5 cm^2/s, experimental = 1.9 x10^-5 cm^2/s). Using VAC I have
> the value of D = 0.9 x 10^-5 cm^2/s. The main problem is not the values
> don´t agree very good with experimental but the values calculated from
> VAC and MSD be so different, while in some papers that I read they are
> very near.
>
> The difference between the simulations I use to calculate MSD and VAC is
> only the output time, where for MSD I have outputs every 200 fs while
> for the VAC simulations the output is made every 1 fs. The models for
> the water and ion are the same. The size of the box too.
>
> I think my problem is in the way I´m integrating the VAC function. I´m
> doing a simple integration and I believe that there is any details in
> this calculation that I don´t know.
>
> You said me something about multiply by cosine of the angular frequency
> and scaling. Could you detail this procedure for me?
>
> Thank you very much for your value help.
>
> Alexandre Suman de Araujo
> asaraujo at if.sc.usp.br
> UIN: 6194055
> IFSC - USP - São Carlos - Brasil
>
>
>
>
> > Can you give me some more details?
> > Are the ions just in bulk water?
> > Or are the ions going from bulk water through some protein and coming
> > to bulk water?
> > If you can explain me the situation, then people here can help you
> better.
> > I recently did some work in these lines too.
> >
> >
> > On 2/23/06, *Alexandre Suman de Araujo* <asaraujo at if.sc.usp.br
> > <mailto:asaraujo at if.sc.usp.br>> wrote:
> >
> >     My calculations is for ions in water and I´m using the mass of the
> >     ions.
> >     My units are correct, a think this is not my problem.
> >     Thank´s
> >
> >     Alexandre Suman de Araujo
> >     asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>
> >     UIN: 6194055
> >     IFSC - USP - São Carlos - Brasil
> >
> >
> >
> >
> >     > IF it is for pure water (bulk), then mass of the water should be
> >     > m=(18e-3)/Ava, where Ava is the Avogadro number.
> >     > KbT/m works out to be 1.3857e+005;
> >     >
> >     > On 2/22/06, * Alexandre Suman de Araujo* <asaraujo at if.sc.usp.br
> >     <mailto:asaraujo at if.sc.usp.br>
> >     > <mailto: asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>>>
> >     wrote:
> >     >
> >     >     Yes, I tried and I had bad values too.
> >     >     I think the Kubo equation is to use in the non-normalized VAC,
> >     >     since the
> >     >     D = kT/M*integral is for normalized ones.
> >     >
> >     >     Alexandre Suman de Araujo
> >     >     asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>
> >     <mailto:asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>>
> >     >     UIN: 6194055
> >     >     IFSC - USP - São Carlos - Brasil
> >     >
> >     >
> >     >
> >     >     Viswanadham Sridhara wrote:
> >     >
> >     >     > Did you try 1/3*your integral
> >     >     >
> >     >     > On 2/22/06, *Alexandre Suman de Araujo* <
> >     asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>
> >     >     <mailto:asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>>
> >     >     > <mailto: asaraujo at if.sc.usp.br
> >     <mailto:asaraujo at if.sc.usp.br> <mailto:asaraujo at if.sc.usp.br
> >     <mailto:asaraujo at if.sc.usp.br>>>>
> >     >     wrote:
> >     >     >
> >     >     >     Hi Gmxers.
> >     >     >
> >     >     >     I´m trying to calculate coefficient diffusion values for
> >     >     ions in
> >     >     >     water.
> >     >     >
> >     >     >     I made some calculations using MSD and the results
> >     were in good
> >     >     >     agreement with experimental values.
> >     >     >
> >     >     >     The problem is when I try to calculate it from
> integration
> >     >     of VAC
> >     >     >     function for the ions, like in Rasaiah paper (J. Chem
> >     Phys.
> >     >     101(8)
> >     >     >     6964).
> >     >     >
> >     >     >     I made 40 simulations of 250 ps with 1 fs time step and
> >     >     output of
> >     >     >     velocities every 1 fs. >From these simulations I
> >     calculated the
> >     >     >     normalized VAC function from these 40 simulations and
> >     >     calculated the
> >     >     >     mean. This methodology is implemented to have a good
> >     >     statistic and a
> >     >     >     more smooth VAC function (without fluctuations that
> could
> >     >     make the
> >     >     >     integral diverge). With this VAC function I use this
> >     equation to
> >     >     >     calculate do diffusion coefficient:
> >     >     >
> >     >     >     D = kT/M*Y, where Y is the integral of the VAC function
> >     >     >
> >     >     >     The problem is that the value calculated from VAC does
> not
> >     >     agree with
> >     >     >     one calculated from MSD.
> >     >     >
> >     >     >     Does anyone knows any trick to perform this kind of
> >     calculation?
> >     >     >     In the
> >     >     >     paper cited above these two values are very near and I´m
> >     >     using the
> >     >     >     same
> >     >     >     methodology.
> >     >     >
> >     >     >     Thank´s!
> >     >     >
> >     >     >     --
> >     >     >     Alexandre Suman de Araujo
> >     >     >     asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>
> >     <mailto: asaraujo at if.sc.usp.br <mailto:asaraujo at if.sc.usp.br>>
> >     >     <mailto: asaraujo at if.sc.usp.br
> >     <mailto:asaraujo at if.sc.usp.br> <mailto:asaraujo at if.sc.usp.br
> >     <mailto:asaraujo at if.sc.usp.br>>>
> >     >     >     UIN: 6194055
> >     >     >     IFSC - USP - São Carlos - Brasil
> >     >     >
> >     >     >     _______________________________________________
> >     >     >     gmx-users mailing list     gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org>
> >     >     <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> >     >     >     <mailto:gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org>>>
> >     >     >     http://www.gromacs.org/mailman/listinfo/gmx-users
> >     >     <http://www.gromacs.org/mailman/listinfo/gmx-users>
> >     >     >     Please don't post (un)subscribe requests to the list.
> >     Use the
> >     >     >     www interface or send it to
> >     gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>
> >     >     <mailto:gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>>
> >     >     >     <mailto: gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>
> >     >     <mailto:gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>>>.
> >     >     >     Can't post? Read
> >     http://www.gromacs.org/mailing_lists/users.php
> >     >     >     <http://www.gromacs.org/mailing_lists/users.php
> >     <http://www.gromacs.org/mailing_lists/users.php>>
> >     >     >
> >     >     >
> >     >     >
> >     >     >
> >     >     > --
> >     >     > Viswanadham Sridhara,
> >     >     > Graduate Research Assistant,
> >     >     > Old Dominion University, "VIRGINIA".
> >     >     >
> >     >
> >
> >------------------------------------------------------------------------
> >     >     >
> >     >     >_______________________________________________
> >     >     >gmx-users mailing list     gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org>
> >     >     <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> >     >     > http://www.gromacs.org/mailman/listinfo/gmx-users
> >     >     >Please don't post (un)subscribe requests to the list. Use the
> >     >     >www interface or send it to gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>
> >     >     <mailto:gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>>.
> >     >     >Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >     >     <http://www.gromacs.org/mailing_lists/users.php>
> >     >     >
> >     >     _______________________________________________
> >     >     gmx-users mailing list    gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org>
> >     >     <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> >     >     http://www.gromacs.org/mailman/listinfo/gmx-users
> >     >     Please don't post (un)subscribe requests to the list. Use the
> >     >     www interface or send it to gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>
> >     >     <mailto:gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>>.
> >     >     Can't post? Read
> >     http://www.gromacs.org/mailing_lists/users.php
> >     <http://www.gromacs.org/mailing_lists/users.php>
> >     >
> >     >
> >     >
> >     >
> >     > --
> >     > Graduate Research Assistant,
> >     > Old Dominion University, "VIRGINIA".
> >     >
> >
> >------------------------------------------------------------------------
> >
> >     >
> >     >_______________________________________________
> >     >gmx-users mailing list    gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org>
> >     > http://www.gromacs.org/mailman/listinfo/gmx-users
> >     >Please don't post (un)subscribe requests to the list. Use the
> >     >www interface or send it to gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>.
> >     >Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >     >
> >     _______________________________________________
> >     gmx-users mailing list     gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org>
> >     http://www.gromacs.org/mailman/listinfo/gmx-users
> >     Please don't post (un)subscribe requests to the list. Use the
> >     www interface or send it to gmx-users-request at gromacs.org
> >     <mailto:gmx-users-request at gromacs.org>.
> >     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >     <http://www.gromacs.org/mailing_lists/users.php>
> >
> >
> >
> >
> > --
> > Old Dominion University, "VIRGINIA".
> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >gmx-users mailing list    gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>

--