ORCA Molecular Dynamics Module
Figure 1: ORCA AIMD Simulation showing how NH3
abstracts a proton from an [Al(H2O)6]3+ complex.
Apart from the underlying electron structure methods, the ORCA MD module also offers some useful features for running different kinds of molecular dynamics simulations. This is a work in progress, and new features are introduced with every release. The following list of features is included in ORCA 4.1, which has been released in December 2018:
- Molecular dynamics simulations can employ Cartesian, distance, angle, and dihedral angle constraints, which are enforced by the RATTLE algorithm.
- The MD module features cells of several geometries (cube, orthorhombic, parallelepiped, sphere, ellipsoid), which can help to keep the system inside of a well-defined volume. The cells have repulsive harmonic walls.
- The cells can be defined as elastic, such that their size adapts to the system. This enables to run simulations under constant pressure.
- Trajectories can be written in XYZ and PDB file format.
- A restart file is written in each simulation step. With this file, simulations can be restarted to seamlessly continue (useful for batch runs or if the job crashed).
- Ability to individually define regions (i. e., subsets of atoms). Regions can be used to thermostat different parts of the system to different temperatures (e. g., cold solute in hot solvent), or to write subset trajectories of selected atoms.
- The energy drift of the simulation is now displayed in every step (in units of Kelvin per atom). Large energy drift can be caused by poor SCF convergence, or by a time step length chosen too large.
The language of the input for the ORCA MD module is SANscript, which is a scripting language for scientific purposes that is currently under development. A full documentation of the language was not yet published. For a first glimpse, please see the SANscript page.
If you have suggestions on useful features which could be implemented in future releases of the ORCA MD module, feel free to contact me via email.
ManualThe manual of the MD module is included in the ORCA manual (section 9.33). Here, you can download a PDF file which only contains the manual of the MD module:
|File||Type / Size||Last Changed|
|ORCA 4.1 MD Manual||.pdf, 301 kiB||Dec 02 2018|
Input ExampleFor a simple AIMD simulation of a water dimer at 300 K with BLYP–D3, please consider the following input example:
! MD BLYP D3 def2-SVP
thermostat berendsen 300_K timecon 10.0_fs
dump position stride 1 filename "trajectory.xyz"
* xyz 0 1
O -2.03740 -1.21799 -0.08342
H -1.06493 -1.04408 -0.02285
H -2.37327 -1.07034 0.83692
O -1.65042 1.84243 0.07893
H -0.72656 1.49786 -0.01029
H -2.07086 1.65422 -0.79801
A library with many input files for ORCA AIMD runs will be established here at a later time.
Please also have a look at the ORCA input library, where many input samples for ORCA can be found.