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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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Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces.
Federico Iori,Stefano Corni +1 more
TL;DR: This article presents a simple approach to introduce metal polarization effects (often termed image effects) in MD simulations by exploiting standard features of bio‐oriented MD codes such as the widely used GROMACS and NAMD.
Journal ArticleDOI
Dissociation of NaCl in water from ab initio molecular dynamics simulations.
TL;DR: Water dipole moments are observed to exhibit little change during dissociation, indicating that description of NaCl with a nonpolarizable force field may be feasible, however, overcoordination of the ion pair at all distances remains as a serious shortcoming of the current classical models.
Journal ArticleDOI
Near UV-Visible electronic absorption originating from charged amino acids in a monomeric protein
Saumya Prasad,Imon Mandal,Shubham Singh,Ashim Paul,Bhubaneswar Mandal,Ravindra Venkatramani,Rajaram Swaminathan +6 more
TL;DR: This work reports 250–800 nm UV-Vis monomeric protein absorption originating from protein backbone– sidechain and sidechain–sidechain charge transfer transitions involving Lys/Glu residues.
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Nucleotide-dependent conformational states of actin
TL;DR: Results suggest a mechanism of allosteric interactions between the nucleotide binding cleft and the DB loop that favors a closed conformation for the bound nucleotide in the ATP and ADP-Pi states, whereas the ADP state favors an open confirmation, both in the monomer and trimer.
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CHARMM-GUI supports the Amber force fields
TL;DR: The development of FF-Converter is presented to prepare Amber simulation inputs with various Amber force fields within the current CHARMM-GUI workflow to support other simulation programs that support the Amber force field.
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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