| 1. |
- Spångberg, Daniel, 1973-, et al.
(författare)
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Trajectory NG : portable, compressed, general molecular dynamics trajectories
- 2011
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Ingår i: Journal of Molecular Modeling. - Berlin/Heidelberg : Springer. - 1610-2940 .- 0948-5023. ; 17:10, s. 2669-2685
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Tidskriftsartikel (refereegranskat)abstract
- We present general algorithms for the compression of molecular dynamics trajectories. The standard ways to store MD trajectories as text or as raw binary floating point numbers result in very large files when efficient simulation programs are used on supercomputers. Our algorithms are based on the observation that differences in atomic coordinates/velocities, in either time or space, are generally smaller than the absolute values of the coordinates/velocities. Also, it is often possible to store values at a lower precision. We apply several compression schemes to compress the resulting differences further. The most efficient algorithms developed here use a block sorting algorithm in combination with Huffman coding. Depending on the frequency of storage of frames in the trajectory, either space, time, or combinations of space and time differences are usually the most efficient. We compare the efficiency of our algorithms with each other and with other algorithms present in the literature for various systems: liquid argon, water, a virus capsid solvated in 15 mM aqueous NaCl, and solid magnesium oxide. We perform tests to determine how much precision is necessary to obtain accurate structural and dynamic properties, as well as benchmark a parallelized implementation of the algorithms. We obtain compression ratios (compared to single precision floating point) of 1:3.3-1:35 depending on the frequency of storage of frames and the system studied.
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| 2. |
- Ahlstrand, Emma, et al.
(författare)
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Interaction energies between metal ions (Zn2+ and Cd2+) and biologically relevant ligands
- 2013
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Ingår i: International Journal of Quantum Chemistry. - Hoboken, NJ : Wiley. - 0020-7608 .- 1097-461X. ; 113:23, s. 2554-2562
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Tidskriftsartikel (refereegranskat)abstract
- Interactions between the group XII metals Zn2+ and Cd2+ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn2+ or Cd2+ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn2+ and Cd2+, in particular at ion–ligand separations that are longer than the equilibrium distances.
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| 3. |
- Amira, S., et al.
(författare)
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Car-Parrinello molecular dynamics simulation of Fe3+(aq)
- 2005
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 109:29, s. 14235-14242
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Tidskriftsartikel (refereegranskat)abstract
- The optimized geometry and energetic properties of Fe(D2O)(n)(3+) clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fell ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell(...)second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.
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| 4. |
- Amira, S., et al.
(författare)
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Derivation and evaluation of a flexible SPC model for liquid water
- 2004
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Ingår i: Chemical Physics. - : Elsevier BV. - 0301-0104 .- 1873-4421. ; 303:3, s. 327-334
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations of a new flexible water model are presented. The potential function is based on the simple point charge (SPC) model combined with an accurate experimental quartic intramolecular potential (CCL). This potential not only reproduces the key structural, dynamical and thermodynamical properties of liquid water, but also generates the correct values for both the absolute O-H vibrational frequency and the gas-to-liquid frequency shift. Thus, the model yields a value of ca. 3420 cm(-1) for the peak maximum of the anharmonic OH stretching band for liquid water (experiment 3400 cm(-1)) and a corresponding gas-to-liquid downshift of -300 cm(-1) (experiment -310 cm(-1)). The paper also emphasizes the importance of parameterizing correctly both the harmonic and anharmonic force constants in the gas-phase when developing flexible water models to be used in the liquid state.
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| 5. |
- Amira, S., et al.
(författare)
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Distorted five-fold coordination of Cu2+ (aq) from a Car-Parrinello molecular dynamics simulation
- 2005
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 7:15, s. 2874-2880
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Tidskriftsartikel (refereegranskat)abstract
- The solvation shell structure and dynamics of a single Cu2+ ion in a periodic box with 32 water molecules under ambient conditions has been investigated using Car-Parrinello molecular dynamics simulations in a time-window of 18 ps. Five-fold coordination with four equidistant equatorial water molecules at 2.00 angstrom and one axial water molecule at 2.45 angstrom from the Cu2+ ion is found. A hole without water molecules is found on the opposite side of the axial water. The ion-water bonding character for the equatorial water molecules is different from that of the axial water molecules, as shown by a localized orbital analysis of the electronic structure. Moreover, the calculated OD stretching vibrational band for the equatorial water molecules lies ca. 175 cm(-1) below the axial-water band, in good agreement with experimental data. The equatorial-water band lies below, and the axial-water band above, the pure liquid D2O band, also in agreement with experimental data.
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| 6. |
- Amira, S., et al.
(författare)
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Molecular dynamics simulation of Fe2+(aq) and Fe3+(aq)
- 2004
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 108:1, s. 496-502
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations of single-ion Fe2+(aq) and Fe3+(aq) solutions have been performed with two rigid-water models (SPC and SPC/E) and a newly constructed SPC-based flexible-water model (SPC+CCL). The SPC+CCL water model in combination with effective Fe2+ and Fe3+ ion-water potentials manages to reproduce many experimental structural and dynamical properties of the solutions. Special attention is given to the large ion-induced frequency shifts of the OH stretching bands, which are also well reproduced by the SPC+CCL model.
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| 7. |
- Amira, S., et al.
(författare)
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OD vibrations and hydration structure in an Al3+(aq) solution from a Car-Parrinello molecular-dynamics simulation
- 2006
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 124:10
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Tidskriftsartikel (refereegranskat)abstract
- The optimized geometry, energetics, and vibrational properties of Al(D2O)(n)(3+) clusters, with n=1,2,4, and 6, have been studied using plane waves, different local basis sets, different methodologies [density-functional theory, MP2, CCSD(T)], and different functionals (BLYP, PBE). Moreover, Car-Parrinello molecular-dynamics (MD) simulations using the BLYP functional, plane waves, and the Vanderbilt ultrasoft pseudopotentials have been performed for an aqueous Al3+ solution with 1 ion and 32 D2O molecules in a periodic box at room temperature, studied for 10 ps. The cluster calculations were performed to pinpoint possible shortcomings of the electronic structure description used in the Car-Parinello MD (CPMD) simulation. For the clusters, the hydration structure and interaction energies calculated with the 'BLYP/plane-wave' approach agree well with high-level ab initio methods but the exchange-correlation functional introduces errors in the OD stretching frequencies (both in the absolute values and in the ion-induced shifts). For the aqueous solution, the CPMD simulation yields structural properties in good agreement with experimental data. The CPMD-simulated OD stretching vibrational band for the first-shell water molecules around Al3+ is strongly downshifted by the influence of the ion and is compared with experimental data from the literature. To make such a comparison meaningful, the influences of a number of systematic effects have been addressed, such as the exchange-correlation functional, the fictitious electron mass, anharmonicity effects, and the small box size in the simulation. Each of these factors (except the last one) is found to affect the OD frequency by 100 cm(-1) or more. The final corrected frequencies agree with experiment within similar to 30 cm(-1) for bulk water but are too little downshifted for the first-shell Al3+(aq) water molecules (by similar to 200 cm(-1)).
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| 8. |
- Barrera, Tony, et al.
(författare)
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Vectorized table driven algorithms for double precision elementary functions using Taylor expansions
- 2009
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Ingår i: APLIMAT 8th international conference. ; 2, s. 171-178
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Konferensbidrag (refereegranskat)abstract
- This paper presents fast implementations of the inverse square root and arcsine, both in double precision. In single precision it is often possible to use a small table and one ordinary Newton-Raphson iteration to compute elementary functions such as the square root. In double precision a substantially larger table is necessary to obtain the desired precision, or, if a smaller table is used, the additional Newton-Raphson iterations required to obtain the precision often requires the evaluation of other expensive elementary functions. Furthermore, large tables use a lot of the cash memory that should have been used for the application code.Obtaining the desired precision using a small table can instead be realised by using a higher order method than the second order Newton-Raphson method. A generalization of Newton's method to higher order is Householder's method, which unfortunately often results in very complicated expressions requiring many multiplications, additions, and even divisions.We show how a high-order method can be used, which only requires a few extra additions and multiplications for each degree of higher order. The method starts from the Taylor expansion of the difference of the value of the elementary function and a starting guess value for each iteration. If the Taylor series is truncated after the second term, ordinary Newton iterations are obtained. In several cases it is possible to algebraically simplify the difference between the true value and the starting guess value. In those cases we show that it is advantageous to use the Taylor series to higher order to obtain the fast convergent method. Moreover, we will show how the coefficients of a Chebyshev polynomial can be fitted to give as little error as possible for the functions close to zero and in the same time reduce the terms in the Taylor expansion.In the paper we benchmark two example implementations of the method on the x86_64 architecture. The first is the inverse square root, where the actual table (to 12 bit precision) is provided by the processor hardware. The inverse square root is important in many application programs, including computer graphics, and explicit particle simulation codes, for instance the Monte Carlo and Molecular Dynamics methods of statistical mechanics. The other example is the arcsine function, which has a slow converging Taylor expansion and where no tables are provided by the hardware. The vectorized versions of the implementations of the inverse square root are 3.5 times faster than compiled code on the Athlon64 and about 5 times faster on the Core 2. The scalar version of the arcsine function is, depending on order and table size, between 2 and 3 times faster than the compiled code, and the vectorized version is between 3 and 4 times faster on the Athlon64, while it is between 4 and 5 times faster than the compiled version on the Core 2.
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| 9. |
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| 10. |
- Gotte, A., et al.
(författare)
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Molecular dynamics study of oxygen self-diffusion in reduced CeO2
- 2007
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Ingår i: Solid State Ionics. - : Elsevier BV. - 0167-2738 .- 1872-7689. ; 178:25-26, s. 1421-1427
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Tidskriftsartikel (refereegranskat)abstract
- The oxygen self-diffusion in partially reduced CeO2 has been investigated by large-scale Molecular Dynamics simulations, in the temperature range between 800 and 2200 K. Simulation boxes with similar to 4100 and similar to 33,000 ions were investigated for randomly distributed oxygen vacancies and Ce3+ ions. Our calculated self-diffusion coefficients vary between 10(-8) and 10(-6) cm(2)/s in the temperature range studied. The activation energy and D-0 values are also reported. The oxygen diffusion mechanism has also been analyzed: only a (< 100 > vacancy mechanism is observed.
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