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A versatile AMBER-Gaussian QM/MM interface through PUPIL.

Juan Torras¹, Gustavo de M Seabra, Erik Deumens

¹Departament d'Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça.Rei 15, 08700-Igualada, Spain.

Journal of Computational Chemistry

|February 14, 2008

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The PUPIL package now links AMBER and Gaussian for computational chemistry. This enables advanced molecular dynamics (MD) simulations on hybrid quantum mechanics/molecular mechanics (QM/MM) systems.

Area of Science:

Computational Chemistry
Materials Science
Biophysics

Background:

The PUPIL package (Program for User Package Interfacing and Linking) was initially designed for multiscale calculations in materials science.
Interfacing diverse computational programs is crucial for complex scientific simulations.

Purpose of the Study:

To extend the PUPIL package for computational chemistry applications.
To enable the integration of AMBER (molecular dynamics) and Gaussian (quantum chemistry) programs.
To facilitate hybrid quantum mechanics/molecular mechanics (QM/MM) simulations.

Main Methods:

Extension of the PUPIL package to interface AMBER and Gaussian.
Application of advanced molecular dynamics (MD) techniques from AMBER.

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Computation of QM forces and energies using Gaussian methods within an MD framework.

Main Results:

Successful interfacing of AMBER and Gaussian via PUPIL.
Demonstration of hybrid QM/MM simulations.
Two example applications: alanine dipeptide in explicit water and steered MD for Angeli's salt dissociation free energy.

Conclusions:

The extended PUPIL package provides a powerful tool for hybrid QM/MM simulations in computational chemistry.
This integration allows leveraging advanced MD techniques with accurate QM calculations.
Enables novel investigations in areas like reaction dynamics and biomolecular systems.