From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Dec 18 2012 - 15:31:25 CST
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
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