Taking the integral of the velocity auto-correlation function multiplied by cosine of the angular frequency and scaling it properly should give the diffusion coefficient as a function of frequency.<br><br><div><span class="gmail_quote">
On 2/22/06, <b class="gmail_sendername">Frederic Leroy</b> <<a href="mailto:frederic.leroy@urv.net">frederic.leroy@urv.net</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;">
What do you mean quantatively by "VAC does not agree with one calculated<br>from MSD"?<br><br><br><br>Alexandre Suman de Araujo wrote:<br><br>> Hi Gmxers.<br>><br>> I´m trying to calculate coefficient diffusion values for ions in 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) 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? In<br>> the paper cited above these two values are very near and I´m using the<br>> same methodology.<br>><br>> Thank´s!<br>>
<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Viswanadham Sridhara,<br>Graduate Research Assistant,<br>Old Dominion University, "VIRGINIA".<br>