NAMD2: Greater Scalability for Parallel Molecular Dynamics

Abstract:The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from

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“…Movie currently supports all versions of AMBER 26 trajectory files, and support for GROMOS 27 and NAMD 28 formats is in progress.…”

Section: Moviementioning

confidence: 99%

UCSF Chimera—A visualization system for exploratory research and analysis

et al. 2004

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“…Therefore, results obtained from these simulations yield only partial information on the experimental cluster size distributions. All simulations were performed using the NAMD [31] package with the CHARMM 2.7 [32,33] force field. The thermalizing effect of the carrier gas was taken into account by assuming that the system evolves according to the Langevin equations of motion in which a noisy environment of a given temperature is coupled to the system and acts as a thermostat.…”

Section: Discussionmentioning

confidence: 99%

Gas-phase formation of large neutral alkaline-earth metal tryptophan complexes

Marksteiner

Haslinger

Sclafani

et al. 2008

J. Am. Soc. Mass Spectrom.

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We report on the first observation of isolated large neutral metal amino acid complexes such as TrpnMek, with Me == Ca, Ba, Sr, cluster combinations covering n = 1. ..33, k = 0..2 and masses beyond 6500 u. The cluster beam is generated using UV laser desorption from a mixed powder of alkaline-earth metal salts and tryptophan inside a cluster mixing chalU1el. The particles are detected using VUV photoionization followed by time-of-flight mass spectroscopy. The enhanced stability of metal amino acid clusters over pure amino acid clusters is substantiated in molecular dynamics simulations by determining the gain in binding energy related to the inclusion of the metal atoms. . The majority of studies so far focused on the generation and use of ionic species. Our work, presented here, focuses on the gas-phase formation of neutral biomolecular clusters as did already some very early studies in the field [1]. Such experiments are often motivated by the desire to better identify the role of solvation and desolvation for the relative importance of various binding forces in organic clusters and molecules [5].The particle's neutrality is also an important criterion in efforts to establish new beam methods for quantum interferometry with molecular matter waves [6-9] as well as for precision metrology on large molecules [10][11][12]. Neutral molecules are much better isolated from any electromagnetic environment and they may therefore propagate coherently, without noticeable perturbation, even in a rather noisy field environment.Biomolecular clusters are exciting study objects for future matter wave experiments as they permit one to scale the mass in well-defined steps, while at the same time changing the internal properties in an intriguing way: the number of possible conformations as well as the number of allowed configurational and vibrational transitions scales exponentially with the size of the cluster [13], and it is still an open question how this will affect de Broglie interferometry [14], which formally considers only the center of mass motion alone. (19]. But it has still remained a challenge to find reproducible methods for photoionizing biomolecules and complexes with masses exceeding 3000 u [17,20,21].The formation and photo-detection of small amino acid [22] and nucleotide clusters [23], both hydrated and solvent-free, were already reported for objects up to 1400 u. Ultracold small bioclusters can be formed by pick-up in helium nano-droplets [24]. Complexes formed between metal atoms and amino acids were also studied to understand their structure [25], their fragmentation pathways [26,27], and metal ion affinities [28].Here we extend these investigations to much larger organometallic complexes composed of up to more than 30 tryptophan molecules with masses exceeding 6500 u, that can still be detected using VUV photoionization and time-of-flight mass spectrometry. ExperimentalWe generate the molecular macroclusters using pulsed laser evaporation and collisional cooling: the pulsed beam of aNd:YAG laser (Quantel...

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“…The protein structure file of the entire system was generated with CHARMM (28). Minimization and molecular dynamics (MD) simulations were carried out with CHARMM27 parameters (28,29) using NAMD (30), due to its demonstrated excellent performance in parallel environments. Periodic boundary conditions and a dielectric constant of 1 were used throughout the simulations.…”

Section: Methodsmentioning

confidence: 99%

Molecular Dissection of a Critical Specificity Determinant within the Amino Acid Editing Domain of Leucyl-tRNA Synthetase

et al. 2003

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A highly conserved threonine residue marks the amino acid binding pocket within the editing active site of leucyl-tRNA synthetases (LeuRSs). It is essential to substrate specificity for the Escherichia coli enzyme in that it blocks the cognate leucine amino acid from binding in the hydrolytic editing active site. We combined mutagenesis and computational approaches to elucidate the molecular role of the critical side chain of this threonine residue. Removal of the terminal methyl group of the threonine side chain by replacement with serine yielded a mutant LeuRS that hydrolyzes Leu-tRNA Leu . Substitution of valine for the conserved threonine conferred similar activities to the wild-type enzyme. However, an additional substitution within the editing active site suggested synergistic interactions with the conserved threonine site that significantly affected amino acid editing. On the basis of our combined biochemical and computational data, we propose that the threonine 252 side chain not only sterically hinders the cognate charged leucine from binding for hydrolysis but also plays a critical role in maintaining an active site geometry that is required for the fidelity of LeuRS.

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NAMD2: Greater Scalability for Parallel Molecular Dynamics

Cited by 2,263 publications

References 48 publications

UCSF Chimera—A visualization system for exploratory research and analysis

UCSF Chimera—A visualization system for exploratory research and analysis

Gas-phase formation of large neutral alkaline-earth metal tryptophan complexes

Molecular Dissection of a Critical Specificity Determinant within the Amino Acid Editing Domain of Leucyl-tRNA Synthetase

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