Re: question about Distance XY

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Sep 13 2011 - 02:50:13 CDT

Dear Hyun,

Your input activates two separate functions:
1) the half-harmonic restraint ("wall") included in the colvar
2) a generic harmonic restraint that keeps the colvar around the value
given by 'centers'

For your purpose, you only need the wall potential, so you can just
remove the 'harmonic' block. The ProjectionXY colvar should do the job
and restrain itself.

Finally, this restraint will not keep the ion in a horizontal plane,
it will keep it within a cylinder of radius 10 A. If you want to
restrain it to a disc-shaped region, you'll need to bias the distanceZ
coordinate for the same atoms.

Cheers,
Jerome

On 13 September 2011 06:27, Song, Hyundeok (songhk) <songhk_at_mail.uc.edu> wrote:
> Dear NAMD users
>
> First I red many postings about Distance XY from mailing list, but I didn't understand some parts.
>
> I want to restrain an ion on XY plane such as the circle of radius 10A
> ex: reference - atom groups from 1 to 32.
>      main - one ion, number 50
>      xydistane between a reference group and an ion.
>
> I included my colvar script. Please read my colvar script. If my script has a problem, please let me know.
> I have two questions.
> 1. Does the harmonic force will not apply as long as an ion is inside the boundary(10A from cm of references)?
>
> 2.  Which value do I choose for  'centers', initial center of restraint ?
> Can I set 'centers' as '0' (A) ?
>
> Initially an ion is inside the circle, and if the harmonic force is applied only if an ion try to escape the circle of radius 10A, setting up 'centers' less than 10A is fine.
> I didn't specify the lowerboundary because it's zero.
>
> Thanks.
>
> Sincerely
> Hyun.
>
> ************************colvar script ****************************************
> colvar {
>   name ProjectionXY
>   upperboundary 10.0
>   upperwallconstant 10.0
>
>   distanceXY {
>      ref {
>         atomNumbersRange {1 - 32 }
>      }
>      main {
>         atomnumbers { 50 }
>      }
>   }
> }
>
>
> harmonic {
> colvars  ProjectionXY
> centers  0.0
> forceConstant 10
> }
>
>

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