About this manual. Many members of the CPMD consortium ( .org/) contributed to this manual. This version of the manual is. Using Molecular Dynamics + Friction forces = the manual way. . be used to create a CPMD input file (see the CPMD user manual for. Send comments and bug reports to [email protected] or. Thierry. [email protected] This manual is for CPMD version
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The following tutorial was adapted and translated from our website with exercises in theoretical chemistry and biochemistry for undergraduate students in chemistry and biochemistry.
Feel free to contact me at axel. If you plan to use this material for your own courses, please include a reference to the master website of our ‘virtual lab’, http: The binary pseudopotential files have been replaced with text-mode files that can be read on all platforms.
The pseudotpotentials and plane wave cutoff have been changed to give much more accurate results at the expense of cpu time. The default temperature has been raised from K to K to get more proton transfers. Modern first priciples Car-Parrinello methods render it possible to simulate complex molecular systems, e. The interactions in such complex systems can not be easily described by fixed, parametrized potentials, like it is usually done for classical molecular dynamics MD simulations.
In a Car-Parrinello MD simulation, however, the interactions are calculated directly from the electron structure in every time step. The forces are obtained from the gradients of the total electronic energy at the positions of the nuclei and thus forming a multi-particle potential.
The determination of the total energy is done in the framework of density functional theory DFT utilizing plane waves basis functions to represent the valence electrons and pseudo-potentials to describe the atomic cores including the inner electrons.
This method allows for an efficient modelling of extended systems, especially crystals or bulk liquids when using periodic boundary conditions. The peculiarity of the Car-Parrinello approach is, that the wave-function is propargated following a ficticious Newtonian dynamic while performing the MD simulation.
Therefore the wave-function does not need to be recalculated in every simulation step and the computational effort is reduced significantly. Performing a Car-Parrinello MD-simulation somewhat resembles classical MD simulations and is usually done along the following steps.
Please remember, that a running simulation does not automatically mean, that the simulation is correctly representing the intended system. Therefore you should carefully examine the outputs of the simulations.
This is especially important for the CPMD runs, since they are extremely cpmmd consuming. So you should carefully plan how to schedule the individual simulations.
The simulation should cover at least ps at a time step of 0. The equilibration works best, if you first run a ps simulation at K and manula that restart to start the K run. For the impatient, there also is a already equilibrated restart. Convert the final configuration from the classical md-simulation into the xyz-format and use the xyz2cpmd. Similar to classical MD-simulations, where you have to provide model potentials e.
For the simulation of water the BLYP functional is recognized as a good choice. Finally you need to specify the size of the basis set. In case of plane waves you give the highest allowed fourier component, selected via the energy cutoff. For the pseudo-potentials given above, a cutoff of 25 Rydberg is recommended.
The manal run was done with CPMD version 3.
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Temperature is controlled by rescaling of the atomic velocities, if the temperature differs more than 50 K from the configured value see the reference output file for what it should look like.
Now you should re-optimize the wavefunction and continue the simulation for more short runs. The ‘quench manuual the Born-Oppenheimer surface’ should not take more than 50 steps. Otherwise stop the simulation with ‘ touch EXIT ‘, cf.
For the given parameters, it should stay around 0. If it becomes much larger, then you need to reoptimize the wavefunction, as you system is about to deviate too far clmd the Born-Oppenheimer Surface.
With the thusly prepared restart you can now run a full production simulation. You can do one of the following simulations:. Use the script traj2xyz. Use the script highlight. Convert the trajectory of the classical md into dcd format and visualize it with VMD see the Moldy manual, on how to do that. Compare what you see to the CPMD run s and discuss similarities and differences between the trajectories.
What are the differences between the individual simulations. Rate the computational effort of all methods. Calculate the oxygen-oxygen and hydrogen-hydrochen pair correlation functions and compare the results with the respective pair correlation functions from the different ab initio and classical MD simulations.
Tutorial: QM/MM MD by CPMD
Some older reference trajectories are available on our FTP-Server. Excerpt from a larger overview article on Car-Parrinello methodology. The full article is availble at http: Printed versions are available on request. Introductory article from Spektrum der Wissenschaft german: Protonenwanderung im virtuellen Manjal.
The nature of the hydrated excess proton in water from Nature and the review of that article from the same journal.
The nature and transport mechanism of hydrated hydroxide ions in aqueous solution again from Nature plus a short review from the same journal and a more elaborate discussion of the article from Angewandte Chemie. Webpage “Water structure and behavior” von Martin Chaplin. Homepage of the Forschergruppe Proton Transport in Bulk Water.
PDF Manual —
Goals of this exercise Insight in the Capabilities of Car-Parrinello molecular dynamics simulations Basic knowledge in setting up and performing Car-Parrinello-simulations Comparison of classical MD with Born-Oppenheimer-MD and Car-Parrinello-MD Grotthuss-mechanism of proton transport in water back to top Introduction Modern first priciples Car-Parrinello methods render it possible to simulate complex molecular systems, e.
Now you can start the calculation with: You can do one of the following simulations: Some older reference trajectories fpmd available on our FTP-Server back to top Additional Information Excerpt from a larger overview article on Car-Parrinello methodology. Further original articles on the same topic: Mon Oct 10