Progress:Zhen

Checked
To be checked
In progress

20161116

1. lipid extraction MD
2. PMF of BN
3. rotation PMF try

20161026

1. tcl script: angle distribution
2. PMF of DMPC/BN angle
3. PMF of membrane and BN
   • DMPC at 290, 295, 300, 305, 310 K
   • POPC at 295, 300, 305, 310 K
   • POPS at 295, 300, 305, 310 K
4. literatures on 2D Materials & Membrane/protein/DNA
5. MoS2 model
6. wiki page for computing resources

20160921

1. Comfirmation of PMF process and results
   • Simulation Time (extend to 25 ns, compare with Langmuir paper of Cheng)
   • Pulling Velocity (compare with Langmuir paper of Cheng)
   • PMF Shape (x distance, y height, why? distance in all windows)
   • Pre-relaxation of lipids bilayer (T, P, xyz, energy)
   • Position constraint of lipids bilayer (compare with others works)
   • Reference Distance (P and COM of bilayer?)
2. Error bar with bootstrap analysis
3. Start SMD for other lipids

20160914

1. PMF Simulation extension
2. MoS2 model building and force field parameters
   • force field parameters in Gromacs
   • membrane component selection: unitary(Langmuir+POPS+DMPC),binary(Langmuir),ternary(JACS)
   • temperature setup in literatures
   • Attention to initial relaxation and test it
3. papers of water desalination
4. Experimental papers on MoS2 Cytotoxicity

20160907

1. Modify PMF results
2. works of Zhiyao & undergraduate dissertation
3. Theories, literatures on umbrella sampling,FEP, free energy
4. literatures on 2D materials/biology: summarizing and proposing

20160826

1. SMD/PMF
   • pulling single DMPC from BN surface
   • pulling single DMPC from DMPC bilayer

20160817

1. C++ learning
2. DMPC/BN model
   • DMPC: Charmm_gui
   • BN Sheet: BN.pdb (Materials Studio) BN.itp (OBGMX)

20160810

1. Coding learning: Python

20160803

1. VMD Tutorials
   • 1
   • 2
2. Relative Shape Anisotropy
   • Concept
   • How to calculate in model

20160727

1. Gromacs Tutorials
   • 1
   • 2
   • 5
   • 7
   • 3
   • 6
   • 4
2. Gromacs Model Building (.pdb/.gro)
   • Packmol
   • Charmm_gui
   • Tools: VMD, GMX-solvate, UltraEdit, etc
3. Gromacs Input files (.itp .top .mdp)
   • restrain
   • constrain
4. Simulation Procedure
   • pbs script
   • gromacs commands
   • completing a simulation of Yonghui
5. Result Analyzing
   • VMD/Tcl Scripting
   • bash scripting
   • Matlab
   • Python
6. Linux
   • basic knowledge and commands
   • bash scripting

20160715

1. Paper reading and summary
   • search for papers on nanomaterials/membrane interactions
   • reading and summary of simulational papers on graphene/membrane interactions
2. Be familiar with Wiki, Combo, and other things in "How To"
   • the use of Wiki
   • the access and use of Combo
   • softwares and scripts
3. To repeat the models of Yonghui
4. 3D pressure profile
   • to know the concept and applications of 3D pressure profile
   • the implementation of 3D pressure profile in models