Tag Archives: Daniel Spångberg

Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field

Authors: Jonàs Sala, Elvira Guàrdia, Jordi Martí, Daniel Spångberg, and Marco Masia

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules.

J. Chem. Phys. 136, 054103 (2012);

DOI: 10.1063/1.3679402

The vibrating hydroxide ion in water

Kersti Hermansson, Philippe A. Bopp, Daniel Spångberg, Ljupco Pejov, Imre Bakó, Pavlin D. Mitev

scienceThe OH ion in water is studied using a CPMD/BLYP + QMelectronic + QMvibrational approach. The ion resides in a cage of water molecules, which are H-bonded among each other, and pinned by H-bonding to the ion’s O atom. The water network keeps the ‘on-top’ water in place, despite the fact that this particular ion-water pair interaction is non-binding. The calculated OH vibrational peak maximum is at ∼3645 cm−1 (experiment ∼3625 cm−1) and the shift with respect to the gas-phase is ∼ +90 cm−1 (experiment +70 cm−1). The waters molecules on each side of the ion (O and H) induce a substantial OH vibrational blueshift, but the net effect is much smaller than the sum. A parabolic ‘frequency-field’ relation qualitatively explains this non-additivity. The calculated ‘in-liquid’ ν(OH) anharmonicity is 85 cm−1.

Chemical Physics Letters, Vol. 514, 2011, Pages 1–15
http://dx.doi.org/10.1016/j.cplett.2011.07.042

Trajectory NG: portable, compressed, general molecular dynamics trajectories

Authors: Daniel Spångberg, Daniel S. D. Larsson, David van der Spoel

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.

Journal of Molecular Modeling October 2011, Volume 17, Issue 10, pp 2669-2685

DOI: 10.1021/ja204100j