about geometrical restrain protein on membrane

From: Liqun Zhang (lxz79_at_case.edu)
Date: Wed Dec 30 2020 - 21:30:37 CST

Dear all:

I want to restrain the protein center of mass distance from the membrane
surface to be no more than 10 A. I know in CHARMM we can set up a
geometrical plane to do that. I am wondering how to do that in namd? I set
up the colvar files as below, and I am wondering if it can work:

colvar {
  name memb_plane
  distanceZ {
    axis (0.0, 0.0, 1.0)
    main {
      atomnumbers {17725 17852 18354 18857 18984 19111 19365 19492 19619
19746 19873 20000 20375 20629 20754 20879 21133 21260 21387 21514 21641
21768 21893 22020}
}
    ref { dummyAtom ( 0.0, 0.0, 0.0 ) }
  }
}

colvar {
  name prot_cyl
  distanceZ {
    axis (0.0, 0.0, 1.0)
    main { atomNumbers { 5 743 1481 2219 2957 3695 4433 5171 5909 6647 7385
8123 8861 9599 10337 11075 11813 12551 13289 14027 14765 15503 16241 16979 }
 }
    ref { dummyAtom ( 0.0, 0.0, 10.0 ) }
  }
}

harmonic {
  colvars memb_plane prot_cyl
  centers 0.0 0.0
  forceConstant 5.0
}

I am wondering if above can work. Thank you for your time!

Lqz

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