From: Liqun Zhang (lxz79_at_case.edu)
Date: Thu Dec 31 2020 - 12:04:59 CST
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> 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 <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>
> *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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