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41.
GROMACS: fast, flexible, and free 总被引:37,自引:0,他引:37
Van Der Spoel D Lindahl E Hess B Groenhof G Mark AE Berendsen HJ 《Journal of computational chemistry》2005,26(16):1701-1718
This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org. 相似文献
42.
43.
We have calculated the self-consistent Green's function for a number of atoms and diatomic molecules. This Green's function is obtained from a conserving self-energy approximation, which implies that the observables calculated from the Green's functions agree with the macroscopic conservation laws for particle number, momentum, and energy. As a further consequence, the kinetic and potential energies agree with the virial theorem, and the many possible methods for calculating the total energy all give the same result. In these calculations we use the finite temperature formalism and calculate the Green's function on the imaginary time axis. This allows for a simple extension to nonequilibrium systems. We have compared the energies from self-consistent Green's functions to those of nonselfconsistent schemes and also calculated ionization potentials from the Green's functions by using the extended Koopmans' theorem. 相似文献
44.
N-(Pyren-1-ylmethyl)-(3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol was synthesised from (3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol and (3R,4S)-4-[(1S)-1,2-dihydroxyethyl] pyrrolidin-3-ol using alkylation with 1-(chloromethyl)pyrene or reductive amination with pyrene-1-carbaldehyde and NaCNBH3. The incorporation of N-(pyren-1-ylmethyl)azasugar moiety into oligodeoxynucleotides (ODN) as a bulge to form an intercalating nucleic acid (INA) induced a slight destabilization of INA-DNA duplex, whereas the INA-RNA duplex was strongly destabilized and 9 degrees C difference per modification in thermal stability between INA-DNA over INA-RNA duplexes was observed. The stabilization of a DNA three way junction (TWJ) was improved when the intercalator moiety was inserted into the junction region as a bulge. 相似文献
45.
Ilse Arendt und Erik Asmus 《Fresenius' Journal of Analytical Chemistry》1960,176(5):321-332
Zusammenfassung Es wird die Möglichkeit einer qualitativen und quantitativen Reinheitsprüfung mit Mitteln der IR-Absorptionsspektroskopie an einer Anzahl von Pyridinderivaten untersucht. Zu diesem Zweck werden die IR-Absorptionsspektren der reinen Substanzen, sowie von binären und ternären Gemischen aufgenommen. Die Spektren werden aus-gewertet und die Nachweisgrenzen angegeben.Dem Verband der Chemischen Industrie und der Deutschen Forschungsgemeinschaft danken wir für die Unterstützung dieser Arbeit. 相似文献
46.
Tam F Syrstad EA Chen X Turecek F 《European journal of mass spectrometry (Chichester, England)》2004,10(6):869-880
Protonated acetamide exists as two planar conformers, the more stable anti-form (anti-1(+)) and the syn-form (syn-1(+)), DeltaG(degree) (298) (anti-->syn) = 10.8 kJ mol(-1). Collisional neutralization of 1(+) produces 1-hydroxy-1-amino-1-ethyl radicals (anti-1 and syn-1) which in part survive for 3.7 micros. The major dissociation of 1 is loss of the hydroxyl hydrogen atom (approximately 95%) which is accompanied by loss of one of the methyl hydrogen atoms (approximately 3%) and loss of the methyl group (approximately 2%). The most favorable dissociation of the OH bond is calculated to be only 34 kJ mol(1) endothermic but requires 88 kJ mol(-1) in the transition state. Other dissociations of 1, e.g., loss of one of the amide hydrogens, methyl hydrogens, and loss of ammonia are calculated to proceed through higher- energy transition states and are not kinetically competitive if proceeding from the ground doublet electronic state of 1. The unimolecular dissociation of 1 following collisional electron transfer is promoted by large Franck-Condon effects that result in 8090 kJ mol(-1) vibrational excitation in the radicals. Radicals 1 are calculated to exoergically abstract hydrogen atoms from acetamide in water, but not in the gas phase. The different reactivity is due to solvent effects that favor the products, (.)CH(2)CONH(2) and CH(3)CH(OH)NH(2), over the reactants. 相似文献
47.
We study wild embeddings of S
1 in S
n which are tame in a sense introduced by Quinn. We show that if is a finitely presented group with H
1()=H
2()=0, then any finiteness obstruction K
0() can be realized on the complement of such an embedded S
1. We also realize trivially symmetric K
–1() obstructions on the complements of such embeddings. For trivially symmetric , the embeddings constructed are shown to be isotopy homogeneous. 相似文献
48.
Adhemar Bultheel Pablo González-Vera Erik Hendriksen Olav Njåstad 《Numerical Algorithms》1992,3(1):91-104
Leta 1,...,a p be distinct points in the finite complex plane ?, such that |a j|>1,j=1,..., p and let \(b_j = 1/\bar \alpha _j ,\) j=1,..., p. Let μ0, μ π (j) , ν π (j) j=1,..., p;n=1, 2,... be given complex numbers. We consider the following moment problem. Find a distribution ψ on [?π, π], with infinitely many points of increase, such that $$\begin{array}{l} \int_{ - \pi }^\pi {d\psi (\theta ) = \mu _0 ,} \\ \int_{ - \pi }^\pi {\frac{{d\psi (\theta )}}{{(e^{i\theta } - a_j )^n }} = \mu _n^{(j)} ,} \int_{ - \pi }^\pi {\frac{{d\psi (\theta )}}{{(e^{i\theta } - b_j )^n }} = v_n^{(j)} ,} j = 1,...,p;n = 1,2,.... \\ \end{array}$$ It will be shown that this problem has a unique solution if the moments generate a positive-definite Hermitian inner product on the linear space of rational functions with no poles in the extended complex plane ?* outside {a 1,...,a p,b 1,...,b p}. 相似文献
49.
It is an open question whether there is a strange attractor for the Henon mapping. We show that for certain maps close to
the Henon map there are strange attractors. 相似文献
50.
Dalia R. Imam Ahmed A. El-Barbary Claus Nielsen Erik B. Pedersen 《Monatshefte für Chemie / Chemical Monthly》2002,133(5):723-734
Summary. 5-Isopropyl-6-naphthyl uracil and 5-isopropyl-6-naphthyl-2-thiouracil were alkylated to give N-1-(ethoxymethyl and methylthiomethyl)
uracil and S2-cyclohexyl-thiouracil, respectively. 5-Ethyl-6-naphthyl uracil and 5-ethyl-6-naphthyl-2-thiouracil afforded N-1-(ethoxymethyl,
methoxy-methyl, methylthiomethyl, acetoxyethoxy methyl and hydroxyethoxy methyl) uracil and S2-((2,2- diethoxyethyl), methoxycarbonylmethyl, ethoxycarbonylpropyl, methylthiomethyl, ethoxymethyl, methyl and cyclohexyl)-thiouracil
upon alkylation.
Received September 25, 2001. Accepted (revised) December 3, 2001 相似文献