Q (software)

Q is a computer software package for molecular dynamics (MD) simulation (current release: Q6). Unlike other MD codes, it has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations. These calculations are based on the methods: empirical valence bond (EVB), free energy perturbation (FEP), and linear interaction energy (LIE), as well as, more recently, also path integral calculations using the bisection quantum classical path (BQCP) approach. The methods in which the program specializes can return quantitative calculations of the energy balance which occurs in proteins and nucleic acids. It can provide insight into key problems in biochemistry such as, energetic details on parts of the translation mechanism in mitochondrial ribosomes (Lind et al. 2013), or details in enzymatic reactions (Mones et al. 2013), among others. The program is similar to GROMACS in being force-field agnostic, meaning that it provides no force-field, but can rather use common force-fields such as CHARMM, AMBER, OPLS, and GROMOS. The software provides one main utility for molecular dynamics called qdyn, and various subprograms such as qprep (to prepare input files from X-ray coordinates), qfep (to process MD calculations for FEP), and others.

Q is a computer software package for molecular dynamics (MD) simulation (current release: Q6). Unlike other MD codes, it has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations. These calculations are based on the methods: empirical valence bond (EVB), free energy perturbation (FEP), and linear interaction energy (LIE), as well as, more recently, also path integral calculations using the bisection quantum classical path (BQCP) approach. The methods in which the program specializes can return quantitative calculations of the energy balance which occurs in proteins and nucleic acids. It can provide insight into key problems in biochemistry such as, energetic details on parts of the translation mechanism in mitochondrial ribosomes (Lind et al. 2013), or details in enzymatic reactions (Mones et al. 2013), among others. The program is similar to GROMACS in being force-field agnostic, meaning that it provides no force-field, but can rather use common force-fields such as CHARMM, AMBER, OPLS, and GROMOS. The software provides one main utility for molecular dynamics called qdyn, and various subprograms such as qprep (to prepare input files from X-ray coordinates), qfep (to process MD calculations for FEP), and others. ==See also== ==References== Marelius J., Kolmodin K., Feierberg I. and Åqvist J., (1998). "Q: A Molecular Dynamics Program for Free Energy Calculations and Empirical Valence Bond Simulations in Biomolecular Systems", Journal of Molecular Graphics and Modelling, 16, 213-225. Lind C., Sund J. and Åqvist J., (2013). "Codon-reading Specificities of Mitochondrial Release Factors and Translation Termination at Non-standard Stop Codons", Nature Communications, 4,2940. Mones L., Tang W., and Florian J., (2013). "Empirical Valence Bond Simulations of the Chemical Mechanism of ATP to cAMP Conversion by Anthrax Edema Factor", Biochemistry, 52, 2672-2682. ==External links==

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