Journal article

QMMMW: A wrapper for QM/MM simulations with QUANTUM ESPRESSO and LAMMPS

We present QMMMW, a new program aimed at performing Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics. The package operates as a wrapper that patches PWscf code included in the QUANTUM ESPRESSO distribution and LAMMPS Molecular Dynamics Simulator. It is designed with a paradigm based on three guidelines: (i) minimal amount of modifications on the parent codes, (ii) flexibility and computational efficiency of the communication layer and (iii) accuracy of the Hamiltonian describing the interaction between the QM and MM subsystems. These three features are seldom present simultaneously in other implementations of QMMM. The QMMMW project is hosted by qe-forge at ( Program summary Program title: QMMMW Catalogue identifier: AEWS_v1_0 Program summary URL: Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 7544822 No. of bytes in distributed program, including test data, etc.: 121657035 Distribution format: tar.gz Programming language: Python, C and Fortran95. Computer: All Linux based workstations and parallel supercomputers. Operating system: GNU/Linux. Classification: 3, 7.7, 16.1, 23. Nature of problem: Calculation of the hybrid quantum mechanics/molecular mechanics of molecular systems. Solution method: With the current patches QMMMW allows the performance of QM/MM simulations with mechanical coupling (i.e. classical point charge based, QM and the MM system interacts electrostatically only at the classical level.) and electrostatic coupling according to the scheme proposed by Laio, VandeVondele and Rothlisberger, J. Chem Phys. 116, 6941 (2002). Restrictions: Only coded for orthorhombic cell. The interactions coupling QM and MM degrees of freedom cannot be bonded. The QM region can only be modeled with PWscf. Unusual features: Minimal amount of modifications to the parent codes. Flexibility and computational efficiency of the communication layer. Accuracy of the Hamiltonian describing the interaction between the QM and MM subsystems. Additional comments: Relevant versions of QUANTUM ESPRESSO and LAMMPS are included in the distribution file and in the number of lines and number of bytes shown. 11111 The distribution file for this program is over 121 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. 11111 Running time: From a few minutes for small molecules on serial machines up to many hours on multiple processors for complex nanosystems with hundreds of atoms. (C) 2015 Elsevier B.V. All rights reserved.


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