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  • PROTEIN FOLDING
  • Molecular Dynamics Simulation
    • ALL ATOM MODEL
      • GROMACS
        • BPTI constant pH_gromacs
        • 1E0Q with gromacs
          • 1E0Q REMD with GROMACS
      • NAMD
        • water_box_namd
      • Amber
        • SMD of 1E0Q
        • Water and Salt Solutions
        • create pure water box for Amber
        • TOP100 AMBER
        • Constant pH simulation of BPTI Implicit(amber)
        • Constant pH simulation of BPTI Explicit(Amber)
        • PH REPLICA EXCHANGE SIMULATION OF BPTI IMPLICIT_AMBER
        • PH REPLICA EXCHANGE SIMULATION OF BPTI EXPLICIT_AMBER
      • CHARMM & MMTSB
        • WATER SOLUTION_CHARMM
        • 1E0Q with CHARMM GPU
        • constant pH simulation BPTI Implicit(charmm)
        • Constant pH Simulation BPTI Explicit(charmm)
        • Replica Exchange Simulation Introduction
        • REPLICA EXCHANGE SIMULATION
          • pH replica exchange simulation of BPTI implicit_charmm
          • Experiment of Rplica Exchange Simulation
          • Temperature REX Simulation of 1E0Q
          • MD simulation of BPTI
            • BPTI constant pH
    • Coarse Grained Models
      • GO Models in CHARMM
      • GO simulation in NAMD
      • Go REX simulation in MMTSB_1E0Q
      • GO_rex_BPTI
      • GO Martini model
        • MARTINI simulation of DPPC
        • Martini model of MORC16
      • Coarse Grained Lipids for Amber(CGLA)
    • Finding Water Bridges
  • LIPID
    • trans-2-aminocyclohexanol
    • Cyclohexane
    • MORC16
  • Catalog
  • 100 proteins bechmark
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MOLC16

May 8, 2015 admin

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  • Linux
  • VMD
  • TOOLSET
  • Water Bridge
  • HBONDS
  • WHAM
  • gnuplot
  • Gromacs
  • CHARMM and MMTSB tool set
  • Amber
  • NAMD
  • force field generation
  • CHARMM TOPOLOGY FILE
  • PH SIMULATION
    • Blocked Amino Acids
  • CHARMM
  • Resources
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