VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon Oct 02 2006 - 12:14:44 CDT

Hi Axel,

I had asked about the min. img. convention when the simulation system is
translated and rotated. As per your suggestion: "you just have to
(temporarily) find a transformation so that
the coordinates are in a simple orthonomal basis again."

------ I created a matrix "{a 0 0 0} {0 b 0 0} {0 0 c 0} {0 0 0 1}" for the
cell basis, and multiplied it with my effective translation/rotation matrix.

1. The resultant does not necessarily have the 4th row/column as {0 0 0 1}.
2. How can I apply the routine orthonomal_basis (from pbcwrap.tcl) to the
resultant 4X4 matrix, as orthonormal_basis can accept 3 vectors?

Some more suggestions will be highly appreciated.
Thank you and regards,
Neelanjana

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.
----------------------------------------------------------------------------------------------
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)
> >
> > Can somebody tell me how to implement the minimum image convention in
> these
> > general cases, where the simulation box is shifted and rotated?
>
> 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.
>