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2.2MolecularDynamicsSimulation
Now, the equations ofmotion have to be calculated for an extended systemwith
3N+1degreesof freedom
r¨i= Fi
mi −s · r˙i (2.11)
where the second term can be seen as a kind of a “friction” originating from the
heat bath.
Then, the extra equationofmotion for theheat bath takes the following form:
s˙= 1
Q (T−Ttarget) (2.12)
Thestrengthof coupling isdeterminedbythe introducedparameterQ, the“mass”
of theheatbath. Toget amore intuitiveparameter for the coupling, a timeparam-
eterτ is introduced.
Q= τ2 ·Ttarget
4π2 (2.13)
The period of oscillation of the kinetic energy between the system and the heat
bath is specifiedby thisparameterτ.
The thermostat is incorporated into the equations ofmotiondirectly in theNosé–
Hoover approach. Therefore, it is an integral part of the integrator and not only
an a posteriori correction. It can be shown that the ensemble generated by the
Nosé–Hoover thermostat is a correct canonical ensemble.
PressureCoupling
Chemical experiments are normally conductedunder conditions of constant pres-
sure. AnNPTensemble isused todescribe such conditions inMDsimulations. In
contrast to the thermostatswhere thevelocities are subject to scaling, thebarostats
scale thevolumeof the simulationbox. This canbedoneequivalently to themeth-
ods described in the previous part. The Berendsen barostat scales the volume of
thebox inadirect fashionandthusshares thesamedrawbackswith theBerendsen
thermostat. Again, amore sophisticatedway is to introduce an additional degree
17
Charge Transport in DNA
Insights from Simulations
- Titel
- Charge Transport in DNA
- Untertitel
- Insights from Simulations
- Autor
- Mario Wolter
- Verlag
- KIT Scientific Publishing
- Datum
- 2013
- Sprache
- englisch
- Lizenz
- CC BY-SA 3.0
- ISBN
- 978-3-7315-0082-7
- Abmessungen
- 17.0 x 24.0 cm
- Seiten
- 156
- Schlagwörter
- Charge Transport, Charge Transfer, DNA, Molecular Dynamics, Quantum Mechanics
- Kategorien
- Naturwissenschaften Chemie
Inhaltsverzeichnis
- Zusammenfassung 1
- Summary 3
- 1 Introduction 5
- 2 TheoreticalBackground 11
- 3 SimulationSetup 39
- 4 DNAUnderExperimentalConditions 49
- 5 ChargeTransport inStretchedDNA 69
- 6 ChargeTransport inMicrohydratedDNA 79
- 7 AParametrizedModel toSimulateCT inDNA 89
- 8 Conclusion 105
- Appendix 111
- A DNAUnderExperimentalConditions 111
- B CTinMicrohydratedDNA 117
- List ofPublications 137