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Scalable Molecular Dynamics with NAMD
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The article was published on 2012-12-14 and is currently open access. It has received 13375 citations till now.read more
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Book ChapterDOI
Molecular Dynamics: New Frontier in Personalized Medicine.
P. Sneha,C. George Priya Doss +1 more
TL;DR: High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship.
Journal ArticleDOI
Gaussian Accelerated Molecular Dynamics in NAMD
TL;DR: Because the boost potential is constructed using a harmonic function that follows Gaussian distribution in GaMD, cumulant expansion to the second order can be applied to recover the original free energy profiles of proteins and other large biomolecules, which solves a long-standing energetic reweighting problem of the previous aMD method.
Journal ArticleDOI
Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions
Alexandru Botan,Fernando Favela-Rosales,Patrick F.J. Fuchs,Matti Javanainen,Matej Kanduč,Waldemar Kulig,Antti Lamberg,Claire Loison,Alexander P. Lyubartsev,Markus S. Miettinen,Luca Monticelli,Jukka Määttä,O. H. Samuli Ollila,Marius Retegan,Tomasz Róg,Hubert Santuz,Joona Tynkkynen +16 more
TL;DR: Focusing on the glycerol backbone and choline headgroups, it is shown that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models, and critically comparing them shows that none of the existing models reached experimental accuracy.
Journal ArticleDOI
Toward the Rational Design of p53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant
Nicolas Basse,Joel L. Kaar,Giovanni Settanni,Andreas C. Joerger,Trevor J. Rutherford,Alan R. Fersht +5 more
TL;DR: The findings provide a blueprint for the design of effective drugs that rescue p53-Y220C and map ligand interaction sites within the mutational cavity, which underpins the importance of considering flexibility of the cavity in screening for optimized ligands.
Journal ArticleDOI
Chemical sensing with switchable transport channels in graphene grain boundaries
Poya Yasaei,Bijandra Kumar,Reza Hantehzadeh,Morteza Kayyalha,Artem Baskin,Nikita Repnin,Canhui Wang,Robert F. Klie,Yong P. Chen,Petr Král,Amin Salehi-Khojin +10 more
TL;DR: This work shows that an isolated graphene grain boundary has ~300 times higher sensitivity to the adsorbed gas molecules than a single-crystalline graphene grain, and opens up new pathways for the design of nanometre-scale highly sensitive chemical detectors.
References
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Journal ArticleDOI
Generalized Gradient Approximation Made Simple
TL;DR: A simple derivation of a simple GGA is presented, in which all parameters (other than those in LSD) are fundamental constants, and only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked.
Journal ArticleDOI
Self-Consistent Equations Including Exchange and Correlation Effects
Walter Kohn,L. J. Sham +1 more
TL;DR: In this paper, the Hartree and Hartree-Fock equations are applied to a uniform electron gas, where the exchange and correlation portions of the chemical potential of the gas are used as additional effective potentials.
Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Journal ArticleDOI
Density-functional exchange-energy approximation with correct asymptotic behavior.
TL;DR: This work reports a gradient-corrected exchange-energy functional, containing only one parameter, that fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
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