AMBER 6 Manuals - CMC/MD

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• Background.
• Preparing to use LES with AMBER
• Using the ADDLES program
• More information on the ADDLES commands and options
• Using the new topology/coordinate files with SANDER
• Case studies: Examples of application of LES
  • Enhanced sampling for individual functional groups: Glucose.
  • Enhanced sampling for a small region: Application of LES to a nucleic acid loop
  • Improving conformational sampling in a small peptide

• Unresolved issues with LES in AMBER
• References for LES and other multiple-copy methods