Software

The FREquency-SElective ANharmonic Mode Analysis eliminates the need for harmonic and quasi-harmonic approximations in the analysis of molecular vibrations. This is of particularly critical for the analysis of highly anharmonic low-frequency vibrations that are thermally excited at room temperature and therefore explore their potential energy surface far beyond a single potential energy minimum.

• Frequency-Selective Anharmonic Mode Analysis of Thermally Excited Vibrations in Proteins, M. A. Sauer and M. Heyden*, J Chem Theory Comput 19, 5481-5490 (2023).

• Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations, S. Mondal, M. A. Sauer and M. Heyden*, J Phys Chem B 128, 7112-7120 (2024).

• Fast Sampling of Protein Conformational Dynamics, M. A. Sauer, S. Mondal, B. Neff, S. Maiti and M. Heyden, (submitted) pre-print: https://arxiv.org/abs/2411.08154

This software package performs a spatially resolved analysis of pairwise additive interactions and intermolecular vibrations on atomistic molecular dynamics simulations in an explicit solvent. Combined with the two-phase thermodynamics (2PT) approach proposed by Goddard and co-workers, this allows us to generate a 3D map of local contributions to the solvation free energy, enthalpy and entropy in addition to various other structural and dynamic properties.

• Signatures of solvation thermodynamics in spectra of intermolecular vibrations, R. A. X. Persson, V. Pattni, A. Singh, S. M. Kast and M. Heyden*, J Chem Theory Comput 13, 4467-4481 (2017).

• Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations, S.-T. Lin, P. K. Maiti, and W. A. Goddard, III, J Phys Chem B 14, 24, 8191–8198 (2010).

This software package allows performing various operations on Gaussian cube files, which are used by 3D-2PT to store water number densities, solvation free energy contributions and other thermodynamic and dynamic parameters of the solvent. Operations include conversion into a simple ASCII table format, +-*/ operations, averaging, application of a Gaussian filter, density scaling, translation and rotation, etc.

This program combines the Aggregation Volume Biased Monte Carlo algorithm from Chen & Siepmann with fully customizable tabulated pairwise interaction potentials between distinct types of particles. This allows to simulate processes such as liquid-liquid phase separation for 100,000 particles on micrometer length scales.

• A Novel Monte Carlo Algorithm for Simulating Strongly Associating Fluids:  Applications to Water, Hydrogen Fluoride, and Acetic Acid, B. Chen and J. I. Siepmann, J Phys Chem B 104, 36, 8725–8734 (2000).

• Improving the Efficiency of the Aggregation−Volume−Bias Monte Carlo Algorithm, B. Chen and J. I. Siepmann, J Phys Chem B 105, 45, 11275–11282 (2001).