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In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics
Figure 2
Global thermostat efficiency test.
Complementary autocorrelation function 
of the end-to-end distance of a DNA molecule simulated with the global Langevin thermostat (black) compared with the same function simulated with the local Langevin thermostat (red). 
is the dimensionless lag-time with 
the thermostat coupling frequency. The DNA molecule is composed of 
rigid cylinders of radius 
and 
. The other parameters of the simulation are given in Table 1. Cylinders are connected by ball-and-socket joints. The chain ends are free to diffuse here.
doi: https://doi.org/10.1371/journal.pcbi.1003456.g002