DsDNA persistence length

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Persistence length of a double-stranded DNA

The example shows how to calculate a persistence length of a double stranded DNA molecule. dsDNA persistence length. The persistence length in this example is calculated using the following formula (see [1] for details):

In the EXAMPLES/PERSISTENCE_LENGTH directory, you will find a setup for calculating the persistence length of a 202 base pairs long dsDNA. Note that for calculating a persistence length of a dsDNA, one needs a large number of decorrelated states. To obtain the states (which will be saved into a trajectory file), run the simulatin program using the prepared input_persistence file:

oxDNA input_persistence .

The program will produce a trajectory.dat file. To analyze the data, use the python script dspl.py:


dspl.py trajectory.dat init.top 10 50

This program will produce a table of correlations between helical vectors, . Using an exponential fit to these data, one can find the persistence length.