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

Vitaly Chaban vvchaban at gmail.com
Mon May 23 22:23:36 CEST 2011


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.

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