AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA and Advanced Micro Devices (AMD) graphics processing unit (GPU) versions as well as Message Passing Interface (MPI) parallel versions. Advanced capabilities include thermodynamic integration, replica exchange MD and accelerated MD methods. A brief update to the software and recently added capabilities is described in this Application Note.

We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H₂O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4–6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.

The thermal Gaussian approximation (TGA) recently developed by Frantsuzov et al. [Chem. Phys. Lett. 381, 117 (2003)] has been demonstrated to be a practical way for approximating the Boltzmann operator $\exp (-\beta \widehat{H})$ for multidimensional systems. In this paper the TGA is combined with semiclassical (SC) initial value representations (IVRs) for thermal time correlation functions. Specifically, it is used with the linearized SC-IVR (LSC-IVR, equivalent to the classical Wigner model), and the “forward-backward semiclassical dynamics” approximation developed by Shao and Makri [J. Phys. Chem. A 103, 7753 (1999); 103, 9749 (1999)]. Use of the TGA with both of these approximate SC-IVRs allows the oscillatory part of the IVR to be integrated out explicitly, providing an extremely simple result that is readily applicable to large molecular systems. Calculation of the force-force autocorrelation for a strongly anharmonic oscillator demonstrates its accuracy, and calculation of the velocity autocorrelation function (and thus the diffusion coefficient) of liquid neon demonstrates its applicability.

The linearized approximation to the semiclassical initial value representation (LSC-IVR) has been used together with the thermal Gaussian approximation (TGA) (TGA/LSC-IVR) [J. Liu and W. H. Miller, J. Chem. Phys. 125, 224104 (2006)] to simulate quantum dynamical effects in realistic models of two condensed phase systems. This represents the first study of dynamical properties of the Ne13 Lennard-Jones cluster in its liquid-solid phase transition region (temperature from 4 to 14 K). Calculation of the force autocorrelation function shows considerable differences from that given by classical mechanics, namely that the cluster is much more mobile (liquidlike) than in the classical case. Liquid para-hydrogen at two thermodynamic state points (25 and 14 K under nearly zero external pressure) has also been studied. The momentum autocorrelation function obtained from the TGA/LSC-IVR approach shows very good agreement with recent accurate path integral Monte Carlo results at 25 K [A. Nakayama and N. Makri, J. Chem. Phys. 125, 024503 (2006)]. The self-diffusion constants calculated by the TGA/LSC-IVR are in reasonable agreement with those from experiment and from other theoretical calculations. These applications demonstrate the TGA/LSC-IVR to be a practical and versatile method for quantum dynamics simulations of condensed phase systems.