IF it is for pure water (bulk), then mass of the water should be m=(18e-3)/Ava, where Ava is the Avogadro number.<br>KbT/m works out to be 1.3857e+005;<br><br><div><span class="gmail_quote">On 2/22/06, <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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Yes, I tried and I had bad values too.<br>I think the Kubo equation is to use in the non-normalized VAC, 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><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* <
<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>> Hi Gmxers.<br>><br>> I´m trying to calculate coefficient diffusion values for ions in
<br>> water.<br>><br>> I made some calculations using MSD and the results were in good<br>> agreement with experimental values.<br>><br>> The problem is when I try to calculate it from integration of VAC
<br>> function for the ions, like in Rasaiah paper (J. Chem Phys. 101(8)<br>> 6964).<br>><br>> I made 40 simulations of 250 ps with 1 fs time step and output of<br>> velocities every 1 fs. >From these simulations I calculated the
<br>> normalized VAC function from these 40 simulations and calculated the<br>> mean. This methodology is implemented to have a good statistic and a<br>> more smooth VAC function (without fluctuations that could make the
<br>> integral diverge). With this VAC function I use this 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 agree with
<br>> one calculated from MSD.<br>><br>> Does anyone knows any trick to perform this kind of calculation?<br>> In the<br>> paper cited above these two values are very near and I´m 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>> UIN: 6194055<br>> IFSC - USP - São Carlos - Brasil<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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<br>Old Dominion University, "VIRGINIA".<br>