Re: Query on colvar distanceZ

From: Karteek Bejagam (karteek4_at_vt.edu)
Date: Sat Nov 19 2016 - 10:12:36 CST

Hi,

I think 0.32 A crossing the boundary is not a problem. It depends on the
wall force constant. Since it adds half harmonic beyond the wall.

Hope this helps.

Best,
Karteek
Dept. of Chemical Engineering,
VirginiaTech, Blacksburg.

On Sat, Nov 19, 2016 at 9:18 AM, Bala subramanian <bala.biophysics_at_gmail.com
> wrote:

> Friends,
> My objective is to restrain an ion-A within a Z-distance of 6.5Ang from
> ion-B. I defined the colvar as below. I dnt apply any other bias on ion-A
>
> colvar {
> name LONGI
> width 0.5
> upperboundary 0.0
> lowerboundary -6.5
>
> lowerwallconstant 100.0
> upperwallconstant 100.0
>
> distanceZ {
> main {
> atomnumbers { 16628 } ; ion-A
> }
> ref {
> atomnumbers { 16625 } ; ion-B ( Z of B > Z of A)
> }
> axis ( 0.0, 0.0, 1.0 )
> }
> }
>
> When i analysed the colvar.traj, i see that the distanceZ varying -6.82 to
> -4.10. I wonder how when i fix the distanceZ to be within -6.5Ang, it
> increase up to -6.82 ?. Is it normal ?. Do i need to use any other criteria
> to achieve distanceZ to be strictly within -6.5.
>
> --
> C. Balasubramanian
>

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