Literature DB >> 15306431

Deterministic and stochastic algorithms for mechanical systems under constraints.

Giovanni Ciccotti1, Galina Kalibaeva.   

Abstract

We discuss the general philosophy underlying the statistical behaviour, the dynamical evolution and the integration of the equations of motion for systems subject to constraints. We also show how all this is related to the treatment of general non-Hamiltonian systems. Then we introduce a family of algorithms derivable from approximations of the evolution operator obtained via the Trotter formula. Generalizing the treatment to time-dependent force fields we also show how one can adapt those algorithms to ordinary stochastic differential equations. Copyright 2004 The Royal Society

Year:  2004        PMID: 15306431     DOI: 10.1098/rsta.2004.1400

Source DB:  PubMed          Journal:  Philos Trans A Math Phys Eng Sci        ISSN: 1364-503X            Impact factor:   4.226


  4 in total

1.  Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.

Authors:  Mey Khalili; Adam Liwo; Anna Jagielska; Harold A Scheraga
Journal:  J Phys Chem B       Date:  2005-07-21       Impact factor: 2.991

2.  Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode.

Authors:  Mey Khalili; Adam Liwo; Franciszek Rakowski; Paweł Grochowski; Harold A Scheraga
Journal:  J Phys Chem B       Date:  2005-07-21       Impact factor: 2.991

3.  Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field.

Authors:  Urszula Kozłowska; Gia G Maisuradze; Adam Liwo; Harold A Scheraga
Journal:  J Comput Chem       Date:  2010-04-30       Impact factor: 3.376

4.  Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.

Authors:  Adam Liwo; Cezary Czaplewski; Adam K Sieradzan; Agnieszka G Lipska; Sergey A Samsonov; Rajesh K Murarka
Journal:  Biomolecules       Date:  2021-09-11
  4 in total

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