From: Aron Broom (broomsday_at_gmail.com)
Date: Mon May 07 2012 - 11:02:30 CDT
can I ask why you need either of these restrictions? The first restriction
at the very least seems pointless. For having the CA atom fixed in place,
I suspect your are trying to mimic AFM experiments or something, but
physics is all relative, if you simply have the colvar be the distance
between the C-terminal CA and the CA of the N-terminus, this is no
different, the relative distance between the two is all that matters
(saying one is fixed is meaningless I would think, maybe I'm missing the
boat though).
In terms of the second restriction, I can see that perhaps this is needed
to accurately recapitulate a pulling experiment, but given the rotational
degrees of freedom around all the residues, I don't think just pulling them
apart along a general distance colvar will be any different than
restricting that pulling along one axis in particular, maybe someone more
mathematically inclined can comment.
~Aron
On Mon, May 7, 2012 at 11:55 AM, Germán Andrés Miño <germino_at_u.uchile.cl>wrote:
> Hi namd2.8 users.
>
> I would like to do and protein unfolding ABF calculation in an water
> box with the following restrictions:
>
> CA atom of the C-terminal fixed in space.
> CA atom of the N-terminal moving along the (0,0,Z) axis.
>
> I have tried with distanceZ (see below) component but my system drift
> away from the Z axis.
>
> I need to minimize the size of the water box (actually a rectangle)
> because limitations in numbers of processors and computational time
> available.
>
> The colvar I am using now is:
>
>
> colvarsTrajFrequency 2000
> colvarsRestartFrequency 20000
>
> colvar {
> name d
>
> width 0.1
>
> lowerboundary 50.36
> upperboundary 380.00
>
> lowerwallconstant 10.0
> upperwallconstant 10.0
>
> distanceZ {
> main { atomNumbers 1921
> }
> ref {
> atomNumbers 959
> }
> axis (0.0, 0.0, 1.0)
>
> }
> }
>
> abf {
> colvars d
> fullSamples 500
> hideJacobian
> }
>
>
> Any suggestion is truly valuated.
> Thanks in advance.
>
> German Miño Galaz.
> germino_at_u.uchile.cl
> Postdoctoral Fellow of Grupo de Namomateriales (www.gnm.cl)
> Departamento de Fisica
> Universidad de Chile.
> Palmeras 3425, Nunoa.
> Santiago Chile
> Tel: 0056-2-978-7439
> Fax: 0056-2-2712973
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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