Xavier, Ones more. The length of the trajectory is 200ps (200 000 time steps). Certainly, both for velocities and displacements. I can ensure this is enough to obtain correct values, no matter Einstein or Green-Kubo formula one uses. Moreover, if you carry out a simulation for 1000ps, nothing will change.
> I tried to determine the length of your velocity C(t) you used to extract > the correlation time. The length of the ACF is 5ps with a step 0.005ps. But it is calculated 200/5 = 40 times and then averaged (just in compliance with its definition). Pls. pay attention that ACF(t) at t > 5ps is fairly zero for any molecular liquid in the ordinary state. > It seems that you used 5 ps for the velocities and 200 ps for the msd! > That might be a reason fot differences, no? Pls. see above. And as for your interest why > frequency to write velocities = 5 > frequency to write coordinates = 100 For MSD we obtain a straight line. Is it not very important which interval to use in this case: 10, 50, 75 or 100. The result (diffusion coefficient) will be the same. Otherwise, ACF does. The most meaningful deviations from zero are observed at t < 2ps. Of course, it is very important to have a small enough step for the velocity output. It is characteristic not only for methanol which I used only as an example. Is it clear now? Again, I'm absolutely sure in all values used for the calculation till the moment when vac.xvg was obtained. But then... I obtain integral. I should divide it by 3 (according to Green-Kubo). But I get quite inconsistent value. Maybe the problem is concerned with units in which velocity is outputted... Will anybody share his expertise in such calculation? :) >>> $ g_msd >>> 2.3 (and it is true) > XP> How much of msd(t) did you use? The part of the curve you use to fit > XP> to Einstein equation will affect enormously the result! > > 200 ps of trajectory was used. It is quite enough. >It depends on many factors: the length of your simulation and the >convergence of your msd curve are two of them. > XP> Here you use 1001 points to integrate! Which result to 1001*0.005fs=5 ps! _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
