Re: about geometrical restrain protein on membrane

From: vermaasj (vermaasj_at_msu.edu)
Date: Thu Dec 31 2020 - 12:08:06 CST

That is certainly a pertinent bit of info. I’d highly advise upgrading to 2.14. In 2.12, the lowerWall, upperWall, and force constant arguments were defined within the colvar itself. https://www.ks.uiuc.edu/Research/namd/2.12/ug/node55.html#SECTION000132200000000000000

-Josh

From: Liqun Zhang <lxz79_at_case.edu>
Date: Thursday, December 31, 2020 at 1:05 PM
To: vermaasj <vermaasj_at_msu.edu>
Cc: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: about geometrical restrain protein on membrane
Hi,
I did the test, but got the error message that
harmonicWalls was not supported.

I used namd 2.12. Thank you!

Lqz

On Thu, Dec 31, 2020 at 9:06 AM vermaasj <vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>> wrote:
To my eyes, your setup looks overly complicated. This would be the colvar I would write to try and keep the protein within 10 Angstroms of a membrane plane:

colvar {
name prot_membrane_distance
distanceZ {
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 {
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 }
}
}
}

harmonicWalls {
name tenangstromwalls
colvars prot_membrane_distance
lowerWalls -10
upperWalls 10
forceConstant 5
}

The key here is to use the “main” and “ref” selections so that you are measuring the relative distance between the two groups, rather than using dummy atoms and an arbitrary reference frame. Just remember to turn wrapping off in NAMD, or the values calculated may not always be what you expect. The harmonic walls constraint defines a flat-bottomed potential that kicks in when you are more than 10 Angstroms away.

-Josh

From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>>
Date: Wednesday, December 30, 2020 at 10:40 PM
To: Namd Mailing List <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>
Subject: namd-l: about geometrical restrain protein on membrane
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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