Difference between revisions of "DsDNA persistence length"

From OxDNA
(Petr's example)
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[[Category:Examples]]
 
[[Category:Examples]]
= Petr's example =
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== Persistence length of a double-stranded DNA ==
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The example shows how to calculate a persistence length of a double stranded DNA molecule.
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dsDNA persistence length. The persistence length in this example is calculated using the following formula (see [http://jcp.aip.org/resource/1/jcpsa6/v134/i8/p085101_s1?bypassSSO=1] for details):
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<math>\langle {\bf n_k} \cdot {\bf n_0} \rangle = \exp(- k \langle l_0 \rangle /L_{ps}).
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</math>
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In the <tt> EXAMPLES/PERSISTENCE_LENGTH </tt> directory, you will find a setup for calculating the persistence length of a 202 base pairs long dsDNA.
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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:
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<tt> oxDNA input_persistence </tt>.
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The program will produce a trajectory.dat file. To analyze the data, use the python script dspl.py:
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<tt> dspl.py trajectory.dat init.top 10 50 </tt>

Revision as of 17:37, 16 April 2012

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