
CHARMM
 Referenced in 115 articles
[sw05953]
 dynamics of large molecules. It performs free energy calculations of mutations and drug binding ... peptides. It uses classical mechanical methods to investigate potential energy surfaces derived from experimental...

LIMbook
 Referenced in 42 articles
[sw14520]
 main instance of line integral methods: the energyconserving RungeKutta methods, also known ... Hamiltonian boundary value methods (HBVMs). The authors go on to address the implementation of HBVMs ... PDEs) and explores extensions of the energyconserving methods. With many examples of applications, this...

Cast3M
 Referenced in 38 articles
[sw12114]
 finite element method. Developed by the French Atomic Energy Commission...

CONTRAfold
 Referenced in 8 articles
[sw17117]
 several decades, free energy minimization methods have been the dominant strategy for single sequence ... probabilistic methods have not replaced free energy minimization methods as the tool of choice...

TINKER
 Referenced in 10 articles
[sw04095]
 pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation...

MCTDH
 Referenced in 32 articles
[sw14837]
 electronic potential energy surfaces. MCTDH by its very nature is an approximate method. However...

GSHMC
 Referenced in 16 articles
[sw02631]
 method to achieve very low rejection rates by using a modified energy, which is preserved ... modified energy is based on backward error results for symplectic timestepping methods. The proposed...

GRIP
 Referenced in 10 articles
[sw12696]
 novel multidimensional forcedirected method together with fast energy function minimization. The algorithm underlying...

Quickstep
 Referenced in 3 articles
[sw26348]
 freely available program package CP2K. The GPW method allows for accurate density functional calculations ... show how derivatives of the GPW energy functional, namely ionic forces and the Kohn–Sham ... computational cost of computing the total energy and the Kohn–Sham matrix is scaling linearly ... parallel performance, and outperforms traditional diagonalisation methods. Energy conserving Born–Oppenheimer dynamics can be performed...

Sturmian
 Referenced in 14 articles
[sw07530]
 state energies of ions. The approximation improves with increasing nuclear charge. The method also allows...

HOPE
 Referenced in 4 articles
[sw32999]
 homotopy optimization method, HOPE, to minimize the potential energy associated ... with a protein model. The method uses the minimum energy conformation of one protein ... determined by a homotopy between the potential energy functions for the two proteins. Ensembles ... compared to a variant of Newton’s method and to simulated annealing...

RAPTOR
 Referenced in 19 articles
[sw09002]
 bound method. The final solution is globally optimal with respect to energy functions. In particular...

EnergyPlus
 Referenced in 10 articles
[sw16969]
 building energy simulation programs around the world are reaching maturity — some use simulation methods ... government supported development of two hourly building energy simulation programs, BLAST and DOE2. Designed ... seen significant advances in analysis and computational methods and power — providing an opportunity for significant ... federal agency began developing a new building energy simulation tool, EnergyPlus, building on development experience...

QSiteFinder
 Referenced in 4 articles
[sw35551]
 SiteFinder: an energybased method for the prediction of protein–ligand binding sites. Results: There...

HERWIG 5.1
 Referenced in 48 articles
[sw02160]
 gluons. Nature of problem: Simulation of high energy particle collisions, especially those in which ... asymptotic and some important subasymptotic contributions. Solution method: Monte Carlo simulation of a variety...

DG_DATH_ELASTIC_V1.0
 Referenced in 5 articles
[sw35139]
 construct energy based, arbitrary order accurate, discontinuous Galerkin spatial discretizations of the linear elastic wave ... equation. The resulting methods are stable and, depending on the choice of numerical flux, conserve ... dissipate the elastic energy. The performance of the method is demonstrated for problems with manufactured...

PROFESS
 Referenced in 6 articles
[sw04202]
 first principles quantum mechanics method to find the groundstate energy of a system ... kinetic energy (unlike KohnSham DFT), and the method scales nearly linearly with the size ... computation and performs the appropriate optimizations. Energies, forces, stresses, material geometries, and electron density configurations...

WENO
 Referenced in 52 articles
[sw12694]
 devices: Performance and comparisons with Monte Carlo methods. In this paper we develop a deterministic ... spherical coordinate system using the energy as one of the coordinate variables, thus reducing...

exactPairingHS
 Referenced in 4 articles
[sw16618]
 particles residing in many energy levels. Solution method: The new HeineStieltjes polynomial approach transforms ... algorithm implemented by the fast NewtonRaphson method with a Monte Carlo sampling procedure ... exact pairing solutions feasible even when more energy levels or heavy nuclei (many pairs...

MUI
 Referenced in 5 articles
[sw18209]
 with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting ... coupling the particlebased energyconserving DPD (eDPD) method with the Finite Element Method...