Dynamics and geometry optimization with ChemShell

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Optimisation Algorithms ● Determination of the search direction ● First-order methods: gradient − Steepest descent − Conjugate gradient − Damped dynamics ● Second order methods: gradient and Hessian − Quasi-Newton methods − RFO − BFGS (accumulated Hessian) − L-BFGS (accumulated Hessian, O(N)) Johannes Kästner STFC Daresbury Lab Transition-State Search Algorithms ● First order saddle points: − Zero gradient − One negative eigenvalue of the Hessian, all others positive ● P-RFO (requires accurate Hessian) ● Dimer method (no Hessian required) ● Newton-Raphson (finds any extremum) Johannes Kästner STFC Daresbury Lab 6
Optimisers in ChemShell Four optimisers available: ● Newopt: flexible optimizer. Methods: BFGS, (P)RFO, DIIS, conjugate gradient, steepest descent, … Coordinate systems: Cartesian or z-matrix ● HDLCopt: fastest for large systems, O(N) Methods: L-BFGS, P-RFO (for transition state search) Coordinate systems: hybrid delocalized internal coordinates ● dimer: TS search with the dimer method ● opt Johannes Kästner STFC Daresbury Lab Johannes Kästner STFC Daresbury Lab 7
Page 1 and 2: L6 Geometry Optimization and Dynami
Page 3 and 4: Free-energy differences: ● Umbrel
Page 5: Coordinate Systems ● Cartesian co
Page 9 and 10: Dimer Method for TS search ● Dime
Page 11 and 12: Molecular Dynamics in ChemShell NVE
Page 13 and 14: Umbrella Sampling ● A number of w
Page 15 and 16: Setup of QM/MM calculations of prot

Dynamics and geometry optimization with ChemShell

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