VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon Oct 09 2006 - 09:48:49 CDT

Hi Olaf,

Sorry about the confusions, but The functions "orhtonormal_basis" and
"basis_change" can be found in the pbcwrap.tcl script.

My problem here is somewhat more complicated than just finding periodic
boundary conditions.
I have a simulation of an 8-residue peptide. During each analysis step (ie.
at each frame), I have to orient each peptide bond such that C=O is along
the y-axis with C at the origin, and the (O=C-N) is in the x-y plane.
This involves 1 translation and 3 rotations, on my entire simulation box. So
now, I cannot simply use the cell basis vectors for finding the min. image
distance bewteen 2 atoms as [x_ij = x_ij - NINT(x_ij/ax) , etc].
The new orthogonal cell basis needs to be determined in place of ax, etc.

As suggested by Axel, I try to apply my transformation matrix (which is 4X4
in vmd) to my original cell basis. I think he said that this basis should
then be orthonormalized to obtain the new values of ax, etc.
This however is not working.....

I would really, really appreciate some help and suggestions in this problem.
Thank you and regards,

Neelanjana Sengupta
*********************************
Graduate Student
Dept. of Chemistry
Univ. of California, Irvine
Irvine, CA 92617
USA
Ph: 1 949 824 9921
email: sengupta_at_uci.edu
*********************************

On 10/9/06, Olaf Lenz <olenz_at_fias.uni-frankfurt.de> wrote:
>
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> Hello!
>
> >> The pbc.tcl script in the script library involves orhtonormalizing a
> >> system, and finding the cell bases in terms of the orthonormal system:
>
> I do not know which script you are referring to: in the script library at
>
> http://www.ks.uiuc.edu/Research/vmd/script_library/
>
>
> I can only find the scripts "pbctools.tcl", "pbcwrap.tcl" and
> "pbcbox.tcl". In none of these, I can the functions that you refer to.
> For handling periodic boundary conditions, I would recommend to use
> these scripts, as they are well documented and combine the efforts of
> three different VMD users.
>
> Best regards
> Olaf
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