On 6/01/2011 2:03 AM, Solomon Berman wrote:
Greetings friends!
I have a question this morning about the g_msd utility related to the output
generated by different flags.
I'm working with an LJ Liquid and am trying to determine the diffusion constant
for the system. I'm employing both the Einstein formulation and the Green Kubo
formula. Obviously, for the Einstein equation, I need the mean square
displacement versus time. The box I am using is cubic, with a length of a side
of 3.602 nm.
Now, when I pass the flag -o for an output (to get the data of the MSD of the
system versus time) with g_msd, and plot the results in xmgrace, I find that
the slope of the resulting graph continuously increases linearly once in the
diffusion regime until the end of the simulation time. However, if I pass the
flag -mol (to get the average MSD per atom) alongside -o, the curve saturates
at two-thirds of the maximum mean square displacement and the slope goes to
zero.
I would like to inquire as to why I receive two different results between "g_msd -o" and
"g_msd -o -mol"? In particular, is it possible that the boundary conditions are treated
differently for each output, where -o ignores the periodic boundary conditions and -mol uses the
periodic boundary conditions? I have tried combing the internet, and the man pages, and haven't
been able to find anything on the reason for the difference in results.
Yes, g_msd -mol leads to a different treatment of periodicity - it
ensures molecules are whole across periodic boundaries. I have updated
the g_msd -h text to note this.
Mark
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