Chemistry Reference
In-Depth Information
Full Period
0.21
0.2
Half-Period
0.19
0.18
0
5
10
15
Slow Force Update Interval (fs)
Figure 4
Sensitivity of the impulse MTS method to slow force update intervals. The
energy error is essentially unchanged from that of velocity Verlet to an update interval
up to 4 fs. For larger update intervals, the energy error becomes erratic, with a notable
jump at the period of the fastest molecular motion.
trajectory shows that the low-frequency motion is correctly resolved by the
impulse MTS method for values of
t
in the stable regime.
Behavior of Langevin-Stabilized Extrapolation Method
on the Model System
Langevin dynamics requires the calculation of a random force vector at
every step. This is implemented for our water dimer in the MATLAB function
dynlang1.m. The best value to select for the collision parameter
is an open
question. In the original work of McCammon, Gelin and Karplus,
39
the choice
was 5/ps. For the water dimer model, we present results using a smaller colli-
sion parameter 2/ps (corresponding to 0.1 in the units presented here). A
power spectrum analysis shows that Langevin dynamics simulations on the
water dimer exhibit essentially the same frequencies as constant-energy simu-
lations, but with broadening of the frequency peaks. This spreading of the
peaks depends upon the magnitude of
g
, with larger values resulting in broader
peaks. This effect can be seen by comparing Figure 3 and Figure 5. We note
that this broadening is especially sensitive for the low-frequency motion,
where the stochastic forces can excite rotations in the dipole about the fixed
atoms. This broadening can be viewed two ways, depending on the nature and
aims of the simulation. If detailed time-dependent dynamical information
about the very low frequency motion is needed, the stochastic forces in Lan-
gevin dynamics blur the picture somewhat. On the other hand this excitation
of low-frequency modes can result in enhanced sampling of the low-frequency
motion, allowing simulations to capture this important motion on a shorter
simulation time scale.
g
