<div>Hi,</div>
<div>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.</div>
<div>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.
</div>
<div>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!</div>
<div>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.
</div>
<div>Thanks,</div>
<div>-Viswanadham <br><br> </div>
<div><span class="gmail_quote">On 2/23/06, <b class="gmail_sendername">Alexandre Suman de Araujo</b> <<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Ok, maybe I was not so clear.<br><br>My system is constituted by only one ion and water molecules (1400). I´m
<br>trying to calculate de diffusion coefficient of this ion in water.<br><br>Using MSD the value is in relative good agreement with experiment (MSD =<br>1.5x10^-5 cm^2/s, experimental = 1.9 x10^-5 cm^2/s). Using VAC I have
<br>the value of D = 0.9 x 10^-5 cm^2/s. The main problem is not the values<br>don´t agree very good with experimental but the values calculated from<br>VAC and MSD be so different, while in some papers that I read they are
<br>very near.<br><br>The difference between the simulations I use to calculate MSD and VAC is<br>only the output time, where for MSD I have outputs every 200 fs while<br>for the VAC simulations the output is made every 1 fs. The models for
<br>the water and ion are the same. The size of the box too.<br><br>I think my problem is in the way I´m integrating the VAC function. I´m<br>doing a simple integration and I believe that there is any details in<br>this calculation that I don´t know.
<br><br>You said me something about multiply by cosine of the angular frequency<br>and scaling. Could you detail this procedure for me?<br><br>Thank you very much for your value help.<br><br>Alexandre Suman de Araujo<br><a href="mailto:asaraujo@if.sc.usp.br">
asaraujo@if.sc.usp.br</a><br>UIN: 6194055<br>IFSC - USP - São Carlos - Brasil<br><br><br><br>Viswanadham Sridhara wrote:<br><br>> Can you give me some more details?<br>> Are the ions just in bulk water?<br>> Or are the ions going from bulk water through some protein and coming
<br>> to bulk water?<br>> If you can explain me the situation, then people here can help you better.<br>> I recently did some work in these lines too.<br>><br>><br>> On 2/23/06, *Alexandre Suman de Araujo* <
<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a><br>> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>>> wrote:<br>><br>> My calculations is for ions in water and I´m using the mass of the
<br>> ions.<br>> My units are correct, a think this is not my problem.<br>> Thank´s<br>><br>> Alexandre Suman de Araujo<br>> <a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br
</a> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>><br>> UIN: 6194055<br>> IFSC - USP - São Carlos - Brasil<br>><br>><br>><br>> Viswanadham Sridhara wrote:<br>
><br>> > IF it is for pure water (bulk), then mass of the water should be<br>> > m=(18e-3)/Ava, where Ava is the Avogadro number.<br>> > KbT/m works out to be 1.3857e+005;<br>> >
<br>> > On 2/22/06, * Alexandre Suman de Araujo* <<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a><br>> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>><br>
> > <mailto: <a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>>>><br>> wrote:<br>> ><br>> > Yes, I tried and I had bad values too.
<br>> > I think the Kubo equation is to use in the non-normalized VAC,<br>> > since the<br>> > D = kT/M*integral is for normalized ones.<br>> ><br>> > Alexandre Suman de Araujo
<br>> > <a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>><br>> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">
asaraujo@if.sc.usp.br</a> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>>><br>> > UIN: 6194055<br>> > IFSC - USP - São Carlos - Brasil<br>> ><br>> >
<br>> ><br>> > Viswanadham Sridhara wrote:<br>> ><br>> > > Did you try 1/3*your integral<br>> > ><br>> > > On 2/22/06, *Alexandre Suman de Araujo* <
<br>> <a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>><br>> > <mailto:<a href="mailto:asaraujo@if.sc.usp.br">
asaraujo@if.sc.usp.br</a> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>>><br>> > > <mailto: <a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a><br>> <mailto:
<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a><br>> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br
</a>>>>><br>> > wrote:<br>> > ><br>> > > Hi Gmxers.<br>> > ><br>> > > I´m trying to calculate coefficient diffusion values for
<br>> > ions in<br>> > > water.<br>> > ><br>> > > I made some calculations using MSD and the results<br>> were in good<br>> > > agreement with experimental values.
<br>> > ><br>> > > The problem is when I try to calculate it from integration<br>> > of VAC<br>> > > function for the ions, like in Rasaiah paper (J. Chem
<br>> Phys.<br>> > 101(8)<br>> > > 6964).<br>> > ><br>> > > I made 40 simulations of 250 ps with 1 fs time step and<br>> > output of
<br>> > > velocities every 1 fs. >From these simulations I<br>> calculated the<br>> > > normalized VAC function from these 40 simulations and<br>> > calculated the
<br>> > > mean. This methodology is implemented to have a good<br>> > statistic and a<br>> > > more smooth VAC function (without fluctuations that could<br>> > make the
<br>> > > integral diverge). With this VAC function I use this<br>> equation to<br>> > > calculate do diffusion coefficient:<br>> > ><br>> > > D = kT/M*Y, where Y is the integral of the VAC function
<br>> > ><br>> > > The problem is that the value calculated from VAC does not<br>> > agree with<br>> > > one calculated from MSD.<br>> > >
<br>> > > Does anyone knows any trick to perform this kind of<br>> calculation?<br>> > > In the<br>> > > paper cited above these two values are very near and I´m
<br>> > using the<br>> > > same<br>> > > methodology.<br>> > ><br>> > > Thank´s!<br>> > ><br>> > > --
<br>> > > Alexandre Suman de Araujo<br>> > > <a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br
</a>><br>> <mailto: <a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>>><br>> > <mailto: <a href="mailto:asaraujo@if.sc.usp.br">
asaraujo@if.sc.usp.br</a><br>> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a>> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">asaraujo@if.sc.usp.br</a><br>> <mailto:<a href="mailto:asaraujo@if.sc.usp.br">
asaraujo@if.sc.usp.br</a>>>><br>> > > UIN: 6194055<br>> > > IFSC - USP - São Carlos - Brasil<br>> > ><br>> > > _______________________________________________
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http://www.gromacs.org/mailing_lists/users.php</a>>><br>> > ><br>> > ><br>> > ><br>> > ><br>> > > --<br>> > > Viswanadham Sridhara,
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