Gone With the Wind

Saturday, October 4, 2008

problem with the solvation

I have the opposite z direction with Todd, so the box size in z direction should be inversed.

The deletion of lipid didn't work so well. So we should first minimize the system, to diminish the overlap of lipid and protein. Then from this structure, we generate the restrained structure.
Posted by Bin Zhang at 5:15 PM
Labels: NAMD_VMD

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Blog Archive

  • ▼  2008 (40)
    • ►  December (1)
    • ►  November (6)
    • ▼  October (22)
      • interpolate missing residues in pdb file
      • periodic table
      • necessary components in protein translocation
      • HOW THE PHOTOCOPIER WORKS
      • LDB problem
      • Align molecule
      • Use pymol to build alpha helix
      • making helix using Modeller
      • Color molecule using electrostatic potential
      • Alpha Helix
      • stop typing pwd using ssh
      • easy way of compiling code?
      • Protein terminus
      • Lipid Tail Selection
      • Make code working on NERSC
      • VMD movie plugin for MAC
      • Wham calculation
      • Hydrophobic effect
      • Non-integer calculation in Shell
      • problem with the solvation
      • wall -- send a message to everybody's terminal.
      • swig wrap c++ and tcl(Makefile)
    • ►  September (11)

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  • Chemistry
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  • Science
  • matlab tips

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Bin Zhang
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