Software
FRESAN Mode Analysis (coming soon)
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).
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).