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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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PLUMED 2: New feathers for an old bird
TL;DR: This work presents PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++), which introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs.
Journal ArticleDOI
CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field
Jumin Lee,Xi Cheng,Jason M. Swails,Min Sun Yeom,Peter Eastman,Justin A. Lemkul,Shuai Wei,Joshua Buckner,Jong Cheol Jeong,Yifei Qi,Sunhwan Jo,Vijay S. Pande,David A. Case,Charles L. Brooks,Alexander D. MacKerell,Jeffery B. Klauda,Wonpil Im +16 more
TL;DR: The optimal simulation protocol for each program has been implemented in CHARMM-GUI and is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.
Proceedings ArticleDOI
Scalable algorithms for molecular dynamics simulations on commodity clusters
Kevin J. Bowers,Edmond Chow,Huafeng Xu,Ron O. Dror,Michael P. Eastwood,Brent A. Gregersen,John L. Klepeis,István Kolossváry,Mark A. Moraes,Federico D. Sacerdoti,John K. Salmon,Yibing Shan,David E. Shaw +12 more
TL;DR: This work presents several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current state-of-the-art codes, including a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time.
Journal ArticleDOI
ACPYPE - AnteChamber PYthon Parser interfacE
TL;DR: ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.
Journal ArticleDOI
CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations
Emilia L. Wu,Xi Cheng,Sunhwan Jo,Huan Rui,Kevin C. Song,Eder M. Dávila-Contreras,Yifei Qi,Jumin Lee,Viviana Monje-Galvan,Richard M. Venable,Jeffery B. Klauda,Wonpil Im +11 more
TL;DR: The new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems are described, including addition of new lipid types, including phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol.
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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