[gmx-users] rapid change in the angle of simulation cell - regd

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 27 09:39:06 CEST 2012

Hi Ramesh,

Did you note how your atoms didn't change their positions? And how you
can still stack them using either set of vectors? It's a great example
of how PBC works. It's not the box that's important, not the vectors,
but the infinite simulation system that results from stacking the unit
cell contents, using the lattice vectors. And there's an infinite
number of lattice vectors that give the same result. Not all of these
vectors are practical to work with from a computational point of view.
What Gromacs does is choosing the vectors that are most convenient to
work with, which is laid down in the rules for box vectors given in
chapter 3 of the manual. This is called the reduced basis of the
lattice. For what you want to do, you need to identify the smallest
difference angle between the lattice vectors in your system and your
reference. The best way to do that is to work with the reduced basis
from the start. Any other set of lattice vectors will give lower
difference angles.
If you don't really get what I'm writing here, you may want to check
Appendix A in http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/03_c3.pdf

Hope it helps,

Tsjerk

On Wed, Sep 26, 2012 at 7:32 AM, ramesh cheerla <rameshgromacs at gmail.com> wrote:
> Dear Gromacs users,
>
>                                  I am performing simulations of  a
> polymer crystal in Gromacs,  for these simulations I have generated a
> triclinic box, and have done one step minimization. In the single step
> minimization itself  the simulation box angle "beta" is varying from
> 125.4 degrees  to 102 degrees. Decrement of beta value by  23.4
> degrees in single step might not be acceptable.  what is the way to
> seize this  large change in beta value ?
> Here I am sending link to the picture of  my system with simulation
> cell before and after minimization of one step(1fs).
>
>  http://researchweb.iiit.ac.in/~bipin.singh/new.png
>
> Can anybody  please go through the image and  provide the  reasonable
> solution, as the angle variations of the simulation cell are one of
> important analyses in my studies.
>
>
>
>
> Regards,
> Ramesh.
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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4