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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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Journal ArticleDOI
Common structural transitions in explicit-solvent simulations of villin headpiece folding.
TL;DR: It is found that the wild-type villin headpiece reliably folds to a native conformation on timescales similar to experimentally observed folding, but that a fast folding double-norleucine mutant shows significantly more heterogeneous behavior.
Journal ArticleDOI
Improving the CHARMM force field for polyunsaturated fatty acid chains.
TL;DR: High-level quantum mechanical calculations are used to improve the dihedral potential of neighboring double bonds, and the corresponding force field is referred to as C36p, and this update in the PUFA force field should allow for accurate MD simulations of PUFA-containing bilayers in the NPT ensemble.
Journal ArticleDOI
MesoBioNano Explorer--a universal program for multiscale computer simulations of complex molecular structure and dynamics.
Ilia A. Solov'yov,Alexander V. Yakubovich,Pavel V. Nikolaev,Ilya Volkovets,Andrey V. Solov’yov +4 more
TL;DR: Despite the universality, the computational efficiency of MBN Explorer is comparable (and in some cases even higher) than the computationalefficiency of other software packages, making MBN explorer a possible alternative to the available codes.
Journal ArticleDOI
A novel crizotinib-resistant solvent-front mutation responsive to cabozantinib therapy in a patient with ROS1-rearranged lung cancer
Alexander Drilon,Alexander Drilon,Romel Somwar,Jacob P. Wagner,Nadeem A. Vellore,Christopher A. Eide,Matthew S. Zabriskie,Maria E. Arcila,Jaclyn F. Hechtman,Lu Wang,Roger S. Smith,Mark G. Kris,Mark G. Kris,Gregory J. Riely,Gregory J. Riely,Brian J. Druker,Thomas O'Hare,Marc Ladanyi,Monika A. Davare +18 more
TL;DR: The discovery of a novel, solvent-front ROS1D2033N mutation in a patient with CD74-ROS1–rearranged lung adenocarcinoma is reported, providing the first example of successful therapeutic intervention with targeted therapy to overcome crizotinib resistance in a ROS1-rearrange cancer.
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Force Field for Molecular Dynamics Computations in Flexible ZIF-8 Framework
TL;DR: In this article, the authors present a full set of force field parameters, based on the AMBER database and on previously computed partial charges, well reproducing the ZIF-8 structural properties over a wide range of temperatures and pressures.
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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