Molecular Dynamics

FlexMD defines the molecular system under study through the MDMolecule class: an instantiation of this class holds all information about the molecular system to be simulated, such as coordinates, topology, and force field parameters (if needed). An MDMolecule object can be initialized from a PDB or XYZ file, by specifying its path at object creation.

An interface to energy evaluators is provided by specialized ForceJob classes, acting as wrappers around the ADF suite of programs. A ForceJob requires an MDMolecule object to be specified at creation. The resulting ForceJob object can either be used directly by the Atomistic Simulation Environment (ASE) [1] library as a calculator object (see examples/scmlib/ASE_emt_h2o) or with the ASEMDPropagator class, which provides methods for running an MD time step using ASE classes. Internally, the propagator sets up the required ASE objects, passes the ForceJob object to them, and retrieves the new positions and velocities. An additional protagonist, an MDManager class instance, coordinates the MD simulation by running the MD steps with the ASEMDPropagator object and writing trajectory information to file.

During creation of an MDManager object, a directory ‘QMMD’ is created, which contains a file TRAJEC00.DCD holding the geometries along the trajectory, a file FTRAJEC00.DCD holding the forces along the trajectory, and finally a file ENERGY00.dat holding the potential and kinetic energy, as well as the temperature throughout the evaluation. To extract the geometries from the trajectory file, the DCDFile class is available, providing methods to read and write geometries to and from a trajectory file in DCD format. The MDManager is also responsible for handling restart of a previous MD evaluation: if a ‘QMMD’ directory is already present at script invocation, the new output files will be assigned the number subsequent to the highest numbered files in that directory. In addition, provided the previous run terminated normally, the restart will continue from the final geometry and velocity of the previous run.

The ADF package contains different electronic structure methods of varying degrees of accuracy and speed. The best-known methods are the ADF Density Functional Theory (DFT) code itself, and the BAND DFT code for periodic systems. FlexMD provides an interface toward both programs. For the interface with ADF, FlexMD makes use of classes from PyADF [2], a scripting framework for efficient quantum chemistry calculations. In addition to ADF and BAND, several semi-empirical methods are included in the ADF suite, such as DFTB and the NDDO type schemes available in the MOPAC package [3]. The ADF suite also provides classical mechanics methods, such as the reactive force field ReaxFF and the simple force field UFF. Interfaces to all of these methods are available in FlexMD. A simple example of a python script for MD using the UFFForceJob class for UFF calculations can be found in the examples directory, under examples/scmlib/flexmd_uff_h2o.

To increase the flexibility of FlexMD, an interface towards force calculations using the NAMD2.8 classical molecular dynamics package is provided (examples/scmlib/namd_h2o). NAMD2.8 is not distributed with the ADF suite, but it is available from a third party to be downloaded and installed (