Matches in DBpedia 2015-10 for { ?s ?p "Q is a Molecular Dynamics (MD) simulation package which, unlike other MD codes, has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations. These calculations are based on the Empirical Valence Bond (EVB) approach, the Free Energy Perturbation (FEP) method, and the Linear Interaction Energy (LIE) method.The three methods that the program specializes on can return quantitative calculations of the energetic 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 the sense that it's force-field agnostic, meaning that it does not provide a force-field itself, but it 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."@en }
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- Q_(software) abstract "Q is a Molecular Dynamics (MD) simulation package which, unlike other MD codes, has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations. These calculations are based on the Empirical Valence Bond (EVB) approach, the Free Energy Perturbation (FEP) method, and the Linear Interaction Energy (LIE) method.The three methods that the program specializes on can return quantitative calculations of the energetic 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 the sense that it's force-field agnostic, meaning that it does not provide a force-field itself, but it 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.".