Density functional tight binding‐based free energy simulations in the DFTB+ program

Abstract

The timescale problem-in which high barriers on the free energy surface trap molecular dynamics simulations in local energy wells-is a key limitation of current reactive MD simulations based on the density functional tight binding (DFTB) potential. Here, we report a new interface between the DFTB+ software package and the PLUMED library for performing DFTB-based free energy calculations. We demonstrate the performance of this interface for 3 archetypal rare-event chemical reactions, (i) intramolecular proton transfer in malonaldehyde, (ii) bowl inversion in corannulene, and (iii) oxygen diffusion on graphene. Using third-order DFTB in conjunction with metadynamics (with/without multiple walkers) and welltempered metadynamics, we report here free energies of activation (ΔG ‡ ) of 13.1 AE 0.4, 48.2 AE 1.7, and 52.0 AE 6.2 kJ mol −1 , respectively, for these processes. In each case, our DFTB free energy barriers and local minima compare favorably with previous literature results, demonstrating the utility of the DFTB+ -PLUMED interface.

Density-functional tight-binding: basic concepts and applications to molecules and clusters

“…Obviously, MD is also be used to follow the dynamical aspects of the system, for instance to simulate a reaction, collision and/or fragmentation (see section 4.7). A Car-Parrinello version of DFTB molecular dynamics was also implemented [176] as well as biased dynamics schemes like metadynamics [177][178][179]. Thermodynamical quantities can also be calculated.…”

Dcdftbmd: Divide‐and‐Conquer Density Functional Tight‐Binding Program for Huge‐System Quantum Mechanical Molecular Dynamics Simulations

“…The DFTB‐based metadynamics simulation is useful for the sampling of rare events, in particular the study related with chemical reactions . Extending to the DC‐DFTB‐based metadynamics simulation enables to treat model system, which is computationally demanding even at the DFTB level.…”

“…The currently implemented CVs are geometric quantities and presented in Supporting Information. The applications of DFTB-based metadynamics are recently growing, [57,[124][125][126][127] yet their investigated system size has been less than a few hundreds of atoms. The combination with the DC method may be feasible to analyze large complex systems as demonstrated in simulation example section.…”

“…The DFTB-based metadynamics simulation is useful for the sampling of rare events, in particular the study related with chemical reactions. [57,127] Extending to the DC-DFTB-based metadynamics simulation enables to treat model system, which is computationally demanding even at the DFTB level. To demonstrate this, we apply the DC-DFTB-based metadynamics simulation to the ketonization of vinyl alcohol to acetaldehyde in water.…”

Hierarchical parallelization of divide‐and‐conquer density functional tight‐binding molecular dynamics and metadynamics simulations

“…[ 50,51 ] Enhanced sampling methods have been recently applied to DFTB‐MD, resulting in novel DFTB‐REMD, [ 52 ] DFTB‐REUS, [ 53,54 ] and DFTB‐MetaD methods. [ 55,56 ]…”