• ## Outreach

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Sep 08 2006 - 14:00:58 CDT

On 9/8/06, Neelanjana Sengupta <senguptan_at_gmail.com> wrote:
> Hi Axel,
>
> Thanks for those pointers. However I need a clarification:
> Suppose I find the effective matrix responsible for the net transformation
> at each step. The way to apply a matrix transformation is with selections,
> \$sel move \$mat_change
>
> How can I create a selection corresponding to the cell basis vectors? Or,

you create a selection for _all_ atoms (in the unitcell), then move/rotated,
apply PBC via the regular orthogonal box criterion, move/rotate back
and go to the next step. if you want to mainain that molecules stay intact,
you have to act a little smarter. basically, you should be able to take
major parts of the pbcwrap script and just feed it your cell vectors.

axel.

> should I write my original orthogonal cell basis as a matrix, upon which I
> operate \$mat_change? What would be the proper way of writing that matrix?
>
> Best regards,
> Neela
>
>
> On 9/7/06, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
> >
> On 9/7/06, Neelanjana Sengupta <senguptan_at_gmail.com > wrote:
> > Hi,
> > I have a simulation of pepitde-solvent system. During my analysis, I am
> > positioning the 4 atoms at each peptide bond in a certain manner at the
> > origin and in the X-Y plane.
> > Due to the operations, and my system is not centered the origin anymore,
> and
> > the simulation box get rotated too. So, the minimum image convention is no
> > longer as straightforward as:
> > x_ij = x_ij - boxL*NINT(x_ij/boxL)
> >
>
> you just have to (temporarily) find a transformation so that
> the coordinates are in a simple orthonomal basis again.
> please have a look at the pbcwrap script from the vmd script
> library. you just need to use some of the lowlevel subroutines
> and feed them your shifted origin and rotated cell vectors.
>
> cheers,
> axel.
>
>
> >
> > With thanks,
> > Neela
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>

```--
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.
```