02542nas a2200349   4500008004100000022001400041245008400055210006900139260006700208300001400275490000700289520144400296653003301740653001601773653001401789653001001803653000701813653001701820653002901837653001101866653001001877100002101887700002101908700002301929700001801952700001801970700001601988700002702004700002102031700002902052856011102081       2013                        eng d  a0192-865100aEffective fragment potential method in Q-CHEM: a guide for users and developers0 aEffective fragment potential method in QCHEM a guide for users a  a111 RIVER ST, HOBOKEN 07030-5774, NJ USAbWILEY-BLACKWELLcMAY  a1060-10700 v343 a<p>A detailed description of the implementation of the effective fragment potential (EFP) method in the Q-CHEM electronic structure package is presented. The Q-CHEM implementation interfaces EFP with standard quantum mechanical (QM) methods such as HartreeFock, density functional theory, perturbation theory, and coupled-cluster methods, as well as with methods for electronically excited and open-shell species, for example, configuration interaction, time-dependent density functional theory, and equation-of-motion coupled-cluster models. In addition to the QM/EFP functionality, a fragment-only feature is also available (when the system is described by effective fragments only). To aid further developments of the EFP methodology, a detailed description of the C++ classes and EFP module's workflow is presented. The EFP input structure and EFP job options are described. To assist setting up and performing EFP calculations, a collection of Perl service scripts is provided. The precomputed EFP parameters for standard fragments such as common solvents are stored in Q-CHEM's auxiliary library; they can be easily invoked, similar to specifying standard basis sets. The instructions for generating user-defined EFP parameters are given. Fragments positions can be specified by their center of mass coordinates and Euler angles. The interface with the IQMOL and WEBMO software is also described. (c) 2013 Wiley Periodicals, Inc.</p>10aeffective fragment potential10aEFP library10ahybrid QM10aIQMOL10aMM10amodular code10anonempirical force field10aQ-CHEM10aWEBMO1 aGhosh, Debashree1 aKosenkov, Dmytro1 aVanovschi, Vitalii1 aFlick, Joanna1 aKaliman, Ilya1 aShao, Yihan1 aGilbert, Andrew, T. B.1 aKrylov, Anna, I.1 aSlipchenko, Lyudmila, V.  uhttps://library.ncl.res.in/content/effective-fragment-potential-method-q-chem-guide-users-and-developers-002796nas a2200229   4500008004100000022001400041245007500055210006900130260007100199300001400270490000800284520199800292100003102290700001902321700002102340700002102361700001802382700001602400700002102416700002902437856010002466       2016                        eng d  a1520-610600aExtension of the effective fragment potential method to macromolecules0 aExtension of the effective fragment potential method to macromol  a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcJUL  a6562-65740 v1203 a<p>The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the C-alpha-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the C-alpha-C and C-alpha-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.</p>1 aGurunathan, Pradeep, Kumar1 aAcharya, Atanu1 aGhosh, Debashree1 aKosenkov, Dmytro1 aKaliman, Ilya1 aShao, Yihan1 aKrylov, Anna, I.1 aSlipchenko, Lyudmila, V.  uhttps://library.ncl.res.in/content/extension-effective-fragment-potential-method-macromolecules