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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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Resources

Gaussian 模块功能及算法选择
【小卒个人文集】写给初学者:小议形式电荷对量化初学者的误导
计算类型及高斯实现方法-4
Binding and Linkage functional chemistry of biological macromolecules
Install Charm++
Amber 分子动力学中文经验谈
分子模拟基础篇
杂谈自由能计算,PM,伞形抽样,WHAM
过渡态、反应路径的计算方法及相关问题
NAMD 入门教程
使用AmberTools+ACPYPE+Gaussian创建小分子GAFF力场的拓扑文件
How to make WordPress Twenty Fourteen theme full width
AMBER 2015 LONDON WORKSHOP - HANDS ON ANALYSIS SESSION ANTECHAMBER TUTORIAL
amber中生成小分子模板(转)
A Concise Guide to CHARMM and the Analysis of Protein Structure and Function
Energy terms in potential function
AMBER file formats

Install Open Babel

  • 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
May 2025
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Groups

  • CHARMM_Dr. Brooks
  • Dr. Stefan Fischer
  • MARTINI_Dr. Siewert-Jan Marrink
  • THE YETHIRAJ RESEARCH GROUP
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