[gmx-users] Re: Velocity autocorrelation function of water using g_velacc

[Vitaly Chaban]

Andrew,

Look here: http://www.sciencedirect.com/science/article/pii/S0022286004002765

I believe the VACs there are the same that you've showed us. So, you
are on the safe side, as for me.

-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216



> If you have time, could you please look at my result at
> http://www.andrew.cmu.edu/user/adeyoung/velacc_may23.pdf and see if you
> think it is a qualitatively reasonable result?  My main concern is the first
> local minimum, which I have labeled with an arrow on the plot.  This minimum
> is in the _positive_ regime, which I believe (but I am not sure) cannot
> correspond to the recoil of atoms when they collide.
>
> In my pdf file I have displayed the parameters I have used for equilibration
> and dynamics.  To summarize, I have used the leap frog algorithm with 2 ns
> equilibration in 1 fs steps, and 5 ns dynamics in 1 fs steps.  For dynamics,
> I have saved configurations every 2 fs.  Although my result from g_velacc
> has velocity autocorrelation frunction data from 0 to 1000 ps, the function
> decays rapidly to zero (as it should, I think, because the velocity rapidly
> decorrelates since the atoms/molecules "forget" their initial velocities),
> so I have plotted only from 0 to 1 ps.  I am running Gromacs version 4.5.4.