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

[Andrew DeYoung]

Hi, 

I have run a simulation of 254 SPC/E water molecules in a cubic box of edge
length 19.660 Angstrom.  I have used the gromacs utility g_velacc to
calculate the velocity autocorrelation function for the motion of only the
oxygen atoms.  When I plot the velocity autocorrelation function versus
time, my result is a curve with more than one local minimum.  

My question is, should I expect having more than one local minimum?  I am
not sure that my result is reasonable.

For example, the Democritus molecular dynamics website gives one example of
a velocity autocorrelation function, although they do not specifically say
what system (water or something else?) or what state (liquid or gas?) was
used: http://www.cse.scitech.ac.uk/ccg/software/Democritus/Theory/vaf.html .
Their plot shows one "strong" local minimum and one "weaker" one; both of
these local minima are in the negative regime.  I am new to this field, but
I believe that the "strong" local minimum corresponds conceptually to the
recoil of the atoms when they collide.  

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.


Thank you very much for your time.

Andrew DeYoung
Carnegie Mellon University