Performance of the Cell processor for biomolecular simulations

The new Cell processor represents a turning point for computing intensive applications. Here, I show that for molecular dynamics it is possible to reach an impressive sustained performance in excess of 30 Gflops with a peak of 45 Gflops for the non-bonded force calculations, over one order of magnitude faster than a single core standard processor

Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes

A general approach for calculating spectral and optical properties of pigment-protein complexes of known atomic structure is presented. The method, that combines molecular dynamics simulations, quantum chemistry calculations and statistical mechanical modeling, is demonstrated by calculating the absorption and circular dichroism spectra of the B800-B850 BChls of the LH2 antenna complex from Rs. molischianum at room temperature. The calculated spectra are found to be in good agreement with the available experimental results. The calculations reveal that the broadening of the B800 band is mainly caused by the interactions with the polar protein environment, while the broadening of the B850 band is due to the excitonic interactions. Since it contains no fitting parameters, in principle, the proposed method can be used to predict optical spectra of arbitrary pigment-protein complexes of known structure.Comment: ReVTeX4, 11 pages, 9 figures, submitted to J. Chem. Phy

A Central Partition of Molecular Conformational Space.III. Combinatorial Determination of the Volume Spanned by a Molecular System

In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into a hierarchical set of cells that can be encoded by the face lattice poset of the arrangement. The model however, lacked explicit rotational symmetry which made impossible to distinguish rotated structures in conformational space. This problem was solved in a second work [physics/0404052] by sorting the elementary 3D components of the molecular system into a set of morphological classes that can be properly oriented in a standard 3D reference frame. This also made possible to find a solution to the problem that is being adressed in the present work: for a molecular system immersed in a heat bath we want to enumerate the subset of cells in conformational space that are visited by the molecule in its thermal wandering. If each visited cell is a vertex on a graph with edges to the adjacent cells, here it is explained how such graph can be built

Intrinsic Conformational Energetics Associated with the Glycosyl Torsion in DNA: A Quantum Mechanical Study

AbstractThe glycosyl torsion (χ) in nucleic acids has long been recognized to be a major determinant of their conformational properties. χ torsional energetics were systematically mapped in deoxyribonucleosides using high-level quantum mechanical methods, for north and south sugar puckers and with γ in the g+ and trans conformations. In all cases, the syn conformation is found higher in energy than the anti. When γ is changed from g+ to trans, the anti orientation of the base is strongly destabilized, and the energy difference and barrier between anti and syn are significantly decreased. The barrier between anti and syn in deoxyribonucleosides is found to be less than 10kcal/mol and tends to be lower with purines than with pyrimidines. With γ=g+/χ=anti, a south sugar yields a significantly broader energy well than a north sugar with no energy barrier between χ values typical of A or B DNA. Contrary to the prevailing view, the syn orientation is not more stable with south puckers than with north puckers. The syn conformation is significantly more energetically accessible with guanine than with adenine in 5-nucleotides but not in nucleosides. Analysis of nucleic acid crystal structures shows that γ=trans/χ=anti is a minor but not negligible conformation. Overall, χ appears to be a very malleable structural parameter with the experimental χ distributions reflecting, to a large extent, the associated intrinsic torsional energetics

Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications

Relevant distance between two different instances of the same potential energy in protein folding

In the context of complex systems and, particularly, of protein folding, a physically meaningful distance is defined which allows to make useful statistical statements about the way in which energy differences are modified when two different instances of the same potential-energy function are used. When the two instances arise from the fact that different algorithms or different approximations are used, the distance herein defined may be used to evaluate the relative accuracy of the two methods. When the difference is due to a change in the free parameters of which the potential depends on, the distance can be used to quantify, in each region of parameter space, the robustness of the modeling to such a change and this, in turn, may be used to assess the significance of a parameters' fit. Both cases are illustrated with a practical example: the study of the Poisson-based solvation energy in the Trp-Cage protein (PDB code 1L2Y).Comment: 20 pages, 6 figures, LaTeX file, elsart style. v1: Aknowledgments modified. v2: y-values of fig. 5 and 6 corrected. v3: Journal-ref added, aknowledgements modified and fig. 1 and 2 correcte

MATCH: An atom‐typing toolset for molecular mechanics force fields

We introduce a toolset of program libraries collectively titled multipurpose atom‐typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A general chemical pattern‐matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges, and force field parameters are achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom‐type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment‐based property prediction. In this work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond charge increment rules derived from one force field can be transferred to another. In addition, using leave‐one‐out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM general force field (Vanommeslaeghe, et al., J Comput Chem 2010, 31, 671), one million molecules from the PubChem database of small molecules are typed, parameterized, and minimized. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/88100/1/JCC_21963_sm_SuppInfo.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/88100/2/21963_ftp.pd

Molecular dynamics simulations of the contact angle between water droplets and graphite surfaces

Wetting is a widespread phenomenon, most prominent in a number of cases, both in nature and technology. Droplets of pure water with initial radius ranging from 20 to 80 [\AA] spreading on graphitic surfaces are studied by molecular dynamics simulations. The equilibrium contact angle is determined and the transition to the macroscopic limit is discussed using Young equation in its modified form. While the largest droplets are almost perfectly spherical, the profiles of the smallest ones are no more properly described by a circle. For the sake of accuracy, we employ a more general fitting procedure based on local averages. Furthermore, our results reveal that there is a possible transition to the macroscopic limit. The modified Young equation is particularly precise for characteristic lengths (radii and contact-line curvatures) around 40 [\AA].Comment: Revised and extended version; http://dx.doi.org/10.1016/j.fluid.2012.07.01