1996
DOI: 10.1021/jp953043o
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Constant Temperature Constrained Molecular Dynamics:  The Newton−Euler Inverse Mass Operator Method

Abstract: The Newton-Euler inverse mass operator (NEIMO) method for internal coordinate molecular dynamics (MD) of macromolecules (proteins and polymers) leads to stable dynamics for time steps about 10 times larger than conventional dynamics (e.g., 20 or 30 fs rather than 1 or 2 fs for systems containing hydrogens). NEIMO is practical for large systems since the computation time scales linearly with the number of degrees of freedom N (instead of the N 3 scaling for conventional constrained MD methods). In this paper we… Show more

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Cited by 77 publications
(100 citation statements)
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“…Optimization of helical bends and kinks. The kinks and bends in each canonical helix was optimized with Newton-Euler inverse mass operator (NEIMO) torsional dynamics (18,19) or Cartesian dynamics (described with the Dreiding FF and Charmm22 charges) for 500 ps at 300 K constant temperature, and we picked the minimum energy conformation from the dynamics. The helical bundle now has helices with bends and kinks.…”
Section: Methodsmentioning
confidence: 99%
“…Optimization of helical bends and kinks. The kinks and bends in each canonical helix was optimized with Newton-Euler inverse mass operator (NEIMO) torsional dynamics (18,19) or Cartesian dynamics (described with the Dreiding FF and Charmm22 charges) for 500 ps at 300 K constant temperature, and we picked the minimum energy conformation from the dynamics. The helical bundle now has helices with bends and kinks.…”
Section: Methodsmentioning
confidence: 99%
“…[20][21][22][23][24][25] Here, we describe the GNEIMO method briefly since it is the basis for the hybrid ICMD method. Since some of the bond lengths and bond angles can be treated as rigid in the hybrid ICMD GNEIMO method, the degrees of freedom in the equations of motion in ICMD method become coupled and have the form…”
Section: Methodsmentioning
confidence: 99%
“…The GNEIMO method forms the basis of the GneimoSim ICMD software package 25 which has been used for a variety of biomolecular applications such as protein folding, 23,24,27 domain motion, 28,29 and refinement of protein homology models. 22,23,30,31 A. Fixman potential to correct for the intrinsic distortion…”
Section: Methodsmentioning
confidence: 99%
“…However, solving for this initial value MD problem is particularly challenging due to the strong covalent bonds between nuclei, requiring painfully small time steps to properly capture the dynamics without generating instability. Turning these covalent bonds into rigid constraints (using RATTLE [4], SHAKE [51], or through internal variables [58] for instance) alleviates the most stringent time step restrictions, but at the cost of having to solve non-linear systems and a significant decrease in parallelizability. Computational efficiency has further increased over the past few years, either through algorithmic improvements (e.g., by computing the more distant interactions less often), or by leveraging specialized hardware for parallel computing (GPU computing).…”
Section: Related Workmentioning
confidence: 99%
“…While implicit integration can partially remedy this restriction, it can also introduce artificial viscosity to the system, damping high frequencies and violating energy conservation. Even symplecticity does not help with stiff problems: as the authors of [22] for molecular dynamics simulations to directly satisfy the stiff bond-length constraints, thus removing the strongest forces in the system [25,51,58]. However, these methods are typically difficult to parallelize and involve tradeoffs between speed, stability, and range of applicability.…”
Section: Stiffness Of Molecular Dynamicsmentioning
confidence: 99%