From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Dec 18 2012 - 23:19:54 CST
So the width of the colvar should probably be 1 if you're planning to use
it for a harmonic constraint, since the force is divided by the width. The
upper and lower boundaries should be the min and max values you want the
colvar to have (which I thought for you was 0 and 5), keep in mind that a
negative number here makes no sense, since this is a distance, it will
always be positive. Then when applying the harmonic constraint you'd set
the center to something in that range (0 to 5) and the forceConstant to
0.0, since you just want a boundary, not to actually force it to any
particular position.
On Tue, Dec 18, 2012 at 6:20 PM, Wang <wybjlu_at_yahoo.cn> wrote:
> Hi Dr Broom,
>
> Thanks for your reply. I did this but I don't know how to check it if it
> is right:
>
> colvar {
> name zsod
> distanceZ {
> main { atomNumbers 60633 }
> ref { atomNumbers 721 723 733 734 735 752 753 754 756 767 768 769 771 778
> 779 }
> axis (0.0, 0.0, 1.0)
> oneSiteSystemForce on
> }
> }
> harmonic {
> colvars zsod
> centers -20.0
> forceConstant 5.0
> }
>
> colvar {
> name cylinder
> upperboundary 20
> upperwallconstant 10.0
> lowerboundary -20
> lowerwallconstant 10.0
> width 5
> distanceXY {
> main { atomNumbers 60633 }
> ref { dummyAtom ( 0.0, 0.0, 0.0 )}
> }
> }
>
>
> Yibo
> -----------------
> Wang Yibo
>
> State Key Laboratory of Theoretical and Computational Chemistry,
> Institute of Theoretical Chemistry,
> Jilin University
> ------------------------------
> *发件人：* Aron Broom <broomsday_at_gmail.com>
> *收件人：* Wang <wybjlu_at_yahoo.cn>
> *抄送：* "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> *发送日期：* 2012年12月18日, 星期二, 2:31 下午
> *主题:* Re: namd-l: cylinder constraint with colvar
>
> you should look into the DistanceXY colvar. You can use the walls of the
> cylinder to define the reference axis (effective Z-axis) so that rotations
> of your cylinder (I'm guessing your cylinder is a membrane protein or
> nanopore or something that might actually move during the simulation).
> Anyway, have a look at that colvar in the manual, I've used it for similar
> things in the past.
>
> ~Aron
>
> On Tue, Dec 18, 2012 at 12:42 PM, Wang <wybjlu_at_yahoo.cn> wrote:
>
>
> Dear all,
>
> Could you guys tell me how to keep an ion in cylinder of radius 5A with
> 'colvar' of NAMD and the center of the cylinder is along z axis, please?
>
> I have to constraint the ion on a plane with harmonic constraint such as:
>
> colvarsTrajFrequency 10
> colvar {
> name zsod
> distanceZ {
> main { atomNumbers 60633 } # the ion
> ref { atomNumbers 721 723 733 734 735 752 753 754 756 767 768 769 771 778
> 779 }
> axis (0.0, 0.0, 1.0)
> oneSiteSystemForce on
> }
> }
> harmonic {
> name my_harm
> colvars zsod
> centers -20.0
> forceConstant 10.0
> }
>
> And at the same time, I need to constraint the ion in the cylinder. The
> top is Z=30A and the bottom is Z=-30A.
>
> Have a nice day,
>
> Yibo
>
> -----------------
> Wang Yibo
>
> State Key Laboratory of Theoretical and Computational Chemistry,
> Institute of Theoretical Chemistry,
> Jilin University
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:51 CST