General Information

CARACAL is a program package for molecular dynamics simulations and rate constant calculations on easy to setup potential energy surfaces. It can both perform classical MD and ring polymer molecular dynamics (RPMD) on potential energy surfaces built upon the quantum mechanically derived force field (QMDFF) by \textsc{Grimme} and the empirical valence bond method by \textsc{Warshel} and others.

QMDFF is able to generate a fully-fledged potential energy description for an arbitrary chemical system, leading to a reasonable description of the accessible energy landscape as well as of bond breakings. With this ability, one can e.g. simulate mechanochemical reaction with a single QMDFF. Two or three QMDFF can be coupled via EVB in order to simulate arbitrary chemical elementary reactions. Based on this simple idea, a list of EVB coupling methods, including the newly-developed transition path corrected reaction path EVB-QMDFF (TREQ) was implemented into the program package. In addition to EVB-QMDFF, a small collection of analytical PES functions for small gas phase systems from the literature was implemented as well as the possibility to call your own energy and gradient routine, if you want to do Caracal calculations with PES information obtained from a quantum chemistry program or arbitrary other sources (machine learning force fields, etc.)

Based upon umbrella samplings of the reaction path, a protocol for black-box calculations of chemical reaction rate constants was implemented. It is possible to predefine the reaction mechanism by chosing one of the preimplemented templates, covering a large part of relevant chemistry. All this can further be fully automated, including the calculation of QM reference data and the setup of the PES (TREQ in that case), such that rate constants and Arrhenius parameters can be obtained for a chemical reaction by only submitting its reaction path!

Besides rate constant calculations, several other tasks can be performed based on molecular dynamics simulations (e.g., applied force vectors or AFM simulations) or static explorations of the PES (TS, IRC optimizations, frequency calculations...).

Caracal currently consists of seven (partially) independent programs, each serving a particular task. They can be divided into three different functionality classes:

Setup of PES functions:

• qmdffgen: Generates a QMDFF from given output of a QM calculation containing the bond orders, charges and frequencies of the reference structure.
• evbopt: Optimizes the parameters of a chosen EVB coupling term (dE, dQ or DG coupling) for a chemical reaction based on two QMDFFs (reactand and product) and reference energies of the reaction path.
• mult_qmdff: The QMDFF of a solvent box is built from given QMDFFs of single solvent molecules.

Application:

• explore: Performs geometry optimizations (minimum and TS), energy, gradient and frequency calculations and reaction path optimizations (IRC) of chemical systems with one of the given PES descriptions.
• dynamic: Molecular dynamics simulations, both classical and RPMD, on QMDFF, EVB-QMDFF, integrated analytical or user-provided potential energy surfaces. Forces can be applied on different collective variables, for sampling of certain chemical processes.
• calc_rate: Calculation of chemical reaction rate constants based on RPMD umbrella samplings and recrossing calculations on one of the available or externally connected potential energy surfaces.

Automatization:

• black_box: With a reaction path as input, reference calculations, PES setup with TREQ and RPMD samplings are done in black-box fashion, resulting in temperature-dependent reaction rate constants and Arrhenius parameters.