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1.
Y. Komeiji 《Journal of Molecular Structure》2000,530(3):237-243
Methods by which to determine conditions for a molecular dynamics (MD) simulation of biological molecules were investigated. Derivation of the optimal parameters of the Ewald summation was described so as to give same precision to the real space, the reciprocal space summations and the van der Waals interaction. Later, the procedure by which to determine the condition of the multiple time step method by RESPA (REference System Propagator Algorithm; Tuckerman et al., 1992, J. Chem. Phys., 97, 1990) was described as exemplified by MD simulations of a solvated β-sheet peptide. The conservation of the total energy in a microcanonical ensemble was measured to investigate the stability of the simulation conditions. The most feasible respective combinations of the time steps were: 0.25 fs for bond, angle and torsion interactions; 2 fs for van der Waals interaction and Ewald real-space summation; and 4 fs for Ewald reciprocal-space summation. Though it retained an acceptable accuracy, this condition accelerated the simulation ten-fold compared to that in which a simple velocity-Verlet method with a time step of 0.25 fs was used. The update of the correction term due to excluded neighbors was then investigated. Better results were obtained when the correction was updated with the real-space than when it was updated with the reciprocal-space summation. Finally, an MD simulation as long as 50 ps performed under the optimal Ewald and RESPA parameters was thus determined. The trajectory showed a good stability, indicating the feasibility of the parameters. 相似文献
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Berk Hess Henk Bekker Herman J. C. Berendsen Johannes G. E. M. Fraaije 《Journal of computational chemistry》1997,18(12):1463-1472
In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1463–1472, 1997 相似文献
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Nicodemo Di Pasquale Richard J. Gowers Paola Carbone 《Journal of computational chemistry》2014,35(16):1199-1207
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Vincent Krutler Wilfred F. van Gunsteren Philippe H. Hünenberger 《Journal of computational chemistry》2001,22(5):501-508
A common method for the application of distance constraints in molecular simulations employing Cartesian coordinates is the SHAKE procedure for determining the Lagrange multipliers regarding the constraints. This method relies on the linearization and decoupling of the equations governing the atomic coordinate resetting corresponding to each constraint in a molecule, and is thus iterative. In the present study, we consider an alternative method, M‐SHAKE, which solves the coupled equations simultaneously by matrix inversion. The performances of the two methods are compared in simulations of the pure solvents water, dimethyl sulfoxide, and chloroform. It is concluded that M‐SHAKE is significantly faster than SHAKE when either (1) the molecules contain few distance constraints (solvent), or (2) when a high level of accuracy is required in the application of the constraints. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 501–508, 2001 相似文献
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《Journal of computational chemistry》2017,38(25):2193-2206
GENeralized‐Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all‐atom and coarse‐grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time‐step integration, and hybrid (CPU + GPU) computing. The string method and replica‐exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free‐energy pathway and obtaining free‐energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. 相似文献
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We describe a method to impose constraints in a molecular dynamics simulation. A technique developed to solve the special case of a linear topology (MILC SHAKE) is hybridized with the SHAKE algorithm. The methodology, which we term MILC‐hybridized SHAKE (or MILCH SHAKE), applies to more complex topologies. Here we consider the important case of all atom models of alkanes. Exploiting the mass difference between carbon and hydrogen we show that for higher alkanes MILCH SHAKE can be an order of magnitude faster than SHAKE. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 相似文献
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A new algorithm is introduced to perform the multiple time step integration of the equations of motion for a molecular system, based on the splitting of the nonbonded interactions into a series of distance classes. The interactions between particle pairs in successive classes are updated at a progressively decreasing frequency. Unlike previous multiple time-stepping schemes relying on distance classes, the present algorithm sorts interacting particle pairs by their next update times rather than by their update frequencies. For this reason, the proposed scheme is extremely flexible with respect to the number of classes that can be employed (up to hundred or more) and the distance dependence of the relative time step size (arbitrary integer function of the distance). It can also easily be adapted to classes defined based on a criterion other than the interparticle distance (e.g., interaction magnitude). Different variants of the algorithm are tested in terms of accuracy and efficiency for simulations of a pure water system (6167 molecules) under truncated-octahedral periodic boundary conditions, and compared to the twin-range method standardly used with GROMOS96 (short- and long-range cutoff distances of 0.8 and 1.4 nm, pair list and intermediate-range interactions updated every five steps). In particular, multiple time-stepping schemes with an accuracy comparable to that of the twin-range method can be designed, that permit to increase the effective (long-range) cutoff distance from 1.4 to 3.0 nm with a performance loss of only about a factor 2. This result is quite encouraging, considering the benefits of doubling the cutoff radius in the context of (bio-)molecular simulations. 相似文献
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When calculating free energy differences between two molecular systems by means of molecular dynamics simulation, accessory potential functions can help eliminate uninteresting configurational entropy contributions, improve convergence, and facilitate reversibility. In this work, we demonstrate that the use of a harmonic potential function to restrain key portions of a molecular system in a free energy perturbation dual-topology molecular dynamics approach dramatically improves convergence and precision of the calculation. Limitations of this technique are illustrated, and its use in conjunction with a fixed bond-length constraint is developed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1278–1283, 1998 相似文献
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Relative free energies for a series of not too different compounds can be estimated accurately from a single simulation of an unphysical reference state that encompasses the characteristic molecular features of the compounds. Previously, this method has been applied to the calculation of free energies of solvation and of ligand binding for small molecules. In the present study we investigate the limits to the accuracy of the method by applying it to a realistic model of the binding of a set of rather large ligands to the protein factor Xa, a key protein in current efforts to design anticoagulation drugs. The evaluation of the binding free energies and conformations of nine derivatives of a biphenylamidino inhibitor leads to insights regarding the effect of the size, flexibility, and character of the unphysical part of the ligand in the reference state on the accuracy of the predicted binding free energies. 相似文献
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Bruce M. Allen Paul K. Predecki Maciej Kumosa 《Journal of computational chemistry》2014,35(9):756-764
Three open‐source applications, NanoEngineer‐1, packmol, and mis2lmp are integrated using an open‐source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open‐source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol‐a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real‐world research requirements and integrated to create a new capability. © 2014 Wiley Periodicals, Inc. 相似文献
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Born‐Oppenheimer ab initio QM/MM molecular dynamics simulation with umbrella sampling is a state‐of‐the‐art approach to calculate free energy profiles of chemical reactions in complex systems. To further improve its computational efficiency, a mass‐scaling method with the increased time step in MD simulations has been explored and tested. It is found that by increasing the hydrogen mass to 10 amu, a time step of 3 fs can be employed in ab initio QM/MM MD simulations. In all our three test cases, including two solution reactions and one enzyme reaction, the resulted reaction free energy profiles with 3 fs time step and mass scaling are found to be in excellent agreement with the corresponding simulation results using 1 fs time step and the normal mass. These results indicate that for Born‐Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, the mass‐scaling method can significantly reduce its computational cost while has little effect on the calculated free energy profiles. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 相似文献
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Equilibrium molecular dynamics (MD) simulations have been performed in both the NVT and NPT ensembles to study the structural and dynamical properties of fully occupied methane clathrate hydrates at 50, 125, and 200 K. Five atomistic potential models were used for water, ranging from fully flexible to rigid polarizable and nonpolarizable. A flexible and a rigid model were utilized for methane. The phonon densities of states were evaluated and the localized rattling modes for the methane molecules were found to couple to the acoustic phonons of the host lattice. The calculated methane density of states was found to be in reasonable agreement with available experimental data. 相似文献
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Matthias Wohlgemuth Dr. Mitsuhiko Miyazaki Dr. Martin Weiler Prof. Makoto Sakai Prof. Otto Dopfer Prof. Masaaki Fujii Prof. Roland Mitrić 《Angewandte Chemie (International ed. in English)》2014,53(52):14601-14604
The dynamics and energetics of water at interfaces or in biological systems plays a fundamental role in all solvation and biological phenomena in aqueous solution. In particular, the migration of water molecules is the first step that controls the overall process in the time domain. Experimentally, the dynamics of individual water molecules is nearly impossible to follow in solution, because signals from molecules in heterogeneous environments overlap. Although molecular dynamics simulations do not have this restriction, there is a lack of experimental data to validate the calculated dynamics. Here, we demonstrate a new strategy, in which the calculated dynamics are verified by measured time‐resolved infrared spectra. The coexistence of fast and slow migrations of water molecules around a CONH peptide linkage is revealed for a model system representative of a hydrate peptide. 相似文献
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Phenylene Ethynylene‐Tethered Perylene Bisimide Folda‐Dimer and Folda‐Trimer: Investigations on Folding Features in Ground and Excited States
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Benjamin Fimmel Minjung Son Young Mo Sung Dr. Matthias Grüne Prof. Dr. Bernd Engels Prof. Dr. Dongho Kim Prof. Dr. Frank Würthner 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(2):615-630
In this work, we have elucidated in detail the folding properties of two perylene bisimide (PBI) foldamers composed of two and three PBI units, respectively, attached to a phenylene ethynylene backbone. The folding behaviors of these new PBI folda‐dimer and trimer have been studied by solvent‐dependent UV/Vis absorption and 1D and 2D NMR spectroscopy, revealing facile folding of both systems in tetrahydrofuran (THF). In CHCl3 the dimer exists in extended (unfolded) conformation, whereas partially folded conformations are observed in the trimer. Temperature‐dependent 1H NMR spectroscopic studies in [D8]THF revealed intramolecular dynamic processes for both PBI foldamers due to, on the one hand, hindered rotation around C?N imide bonds and, on the other hand, backbone flapping; the latter process being energetically more demanding as it was observed only at elevated temperature. The structural features of folded conformations of the dimer and trimer have been elucidated by different 2D‐NMR spectroscopy (e.g., ROESY and DOSY) in [D8]THF. The energetics of folding processes for the PBI dimer and trimer have been assessed by calculations applying various methods, particularly the semiempirical PM6‐DH2 and the more sophisticated B97D approach, in which relevant dispersion corrections are included. These calculations corroborate the results of NMR spectroscopic studies. Folding features in the excited states of these PBI foldamers have been characterized by using time‐resolved fluorescence and transient absorption spectroscopy in THF and CHCl3, exhibiting similar solvent‐dependent behavior as observed for the ground state. Interestingly, photoinduced electron transfer (PET) process from electron‐donating backbone to electron‐deficient PBI core for extended, but not for folded, conformations was observed, which can be explained by a fast relaxation of excited PBI stacks in the folded conformation into fluorescent excimer states. 相似文献
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We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all‐atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time‐step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calculation, pressure coupling with a “densostat,” and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, atomic instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA molecular modeling and simulation program from www.YASARA.org . © 2015 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. 相似文献
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Using the path integral formalism or the Feynman-Hibbs approach, various expressions for the free energy of quantization for a molecular system in the condensed phase can be derived. These lead to alternative methods to directly compute quantization free energies from molecular dynamics computer simulations, which were investigated with an eye to their practical use. For a test system of liquid neon, two methods are shown to be most efficient for a direct evaluation of the excess free energy of quantization. One of them makes use of path integral simulations in combination with a single-step free energy perturbation approach and was previously reported in the literature. The other method employs a Feynman-Hibbs effective Hamiltonian together with the thermodynamic integration formalism. However, both methods are found to give less accurate results for the excess free energy of quantization than the estimate obtained from explicit path integral calculations on the excess free energy of the neon liquid in the classical and quantum mechanical limit. Suggestions are made to make both methods more accurate. 相似文献
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We propose a novel analysis method of ab initio molecular dynamics (AIMD) simulation using a continuous wavelet transform (c-WT) technique. The c-WT technique, one of the time-frequency signal analysis methods, provides a clear view of the dynamical information in time developments. Combined with the auto-correlation function of velocity by AIMD simulation, c-WT analysis enables us to well understand dynamical distribution, such as the vibrational properties following a change of electronic structure in a molecular system. As a practical application, AIMD simulation of core-excited BF(3) (B1s --> 2a(2) (')) is illustrated. AIMD simulation leads to the change of vibrational motion as well as structural deformation by core-excitation. The c-WT analysis clarifies the relationship between structural deformation and the related significant vibrational modes in core-excitation within 50 fs. 相似文献