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Home > Molecular Dynamics Software: List of Software for Molecular Mechanics Modeling, Charmm, Amber, Molecular Design Software, Gromacs, Mdynamix(English)
Molecular Dynamics Software: List of Software for Molecular Mechanics Modeling, Charmm, Amber, Molecular Design Software, Gromacs, Mdynamix(English)

Molecular Dynamics Software: List of Software for Molecular Mechanics Modeling, Charmm, Amber, Molecular Design Software, Gromacs, Mdynamix(English)

          
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About the Book

Purchase includes free access to book updates online and a free trial membership in the publisher's book club where you can select from more than a million books without charge. Chapters: List of Software for Molecular Mechanics Modeling, Charmm, Amber, Molecular Design Software, Gromacs, Mdynamix, Desmond, Ascalaph Designer, List of Nucleic Acid Simulation Software, Tinker, Gromos, Moscito, D. E. Shaw Research, Yasara, Lammps, Namd, Macromodel, Xmd, X-Plor. Excerpt: AMBER is used to minimize the bond stretching energy of this ethane molecule. AMBER (an acronym for Assisted Model Building with Energy Refinement ) is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman 's group at the University of California, San Francisco . AMBER is also the name for the molecular dynamics software package that simulates these force fields. It is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Tom Darden at NIEHS, Ken Merz at Florida, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals. Force field The term "AMBER force field " generally refers to the functional form used by the family of AMBER force fields. This form includes a number of parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name. Functional form The functional form of the AMBER force field is Note that despite the term force field, this equation defines the potential energy of the system; the force is the derivative of this potential with respect to position. The meanings of right hand side terms are: The form of the van der Waals energy is evinced by the equilibrium distance ( ) and well depth ( ). The factor of 2 ensures that the equilibrium distance is . The form of the electrostatic energy used here assumes that the charges due to the protons and electrons in...


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Product Details
  • ISBN-13: 9781155631110
  • Publisher: Books LLC
  • Publisher Imprint: Books LLC
  • Depth: 6
  • Language: English
  • Returnable: N
  • Spine Width: 4 mm
  • Weight: 122 gr
  • ISBN-10: 1155631110
  • Publisher Date: 05 May 2010
  • Binding: Paperback
  • Height: 152 mm
  • No of Pages: 74
  • Series Title: English
  • Sub Title: List of Software for Molecular Mechanics Modeling, Charmm, Amber, Molecular Design Software, Gromacs, Mdynamix
  • Width: 229 mm


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