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

[ramesh cheerla]

Dear Tsjerk,

                      I am very thankful to you for your reply and sorry
for delay as  it has taken much time to understand the things properly.
I have gone through the material that you have attached with this mail that
is really useful.
Now I have understood that large  change in beta value of my simulation
cell  is because of Gromacs's  convenient  way to choose the periodic
boundary conditions and not because of forcefield that I have used.
  From your mail and Gromacs manual I have understood that, the box vectors
of a simulation unit cell should satisfy the three conditions given in the
chapter-3 of manual( eqs:3.1,3.2 & 3.3) if simulation unit cell satisfies
these conditions then that is called the reduced basis lattice(am i correct
? ).  According to you if we start the simulations with reduced basis
lattice then the difference in the angles of reference system and the
simulated system will become lesser.  For my simulations I have generated
simulation cell by using editconf as :
      editconf  -f  input.gro   -bt  triclinic    -box  3.30  2.7  8.055
  -angles 90 125.4  90  -o output_box.gro
then I have extracted box vectors from the output.gro and  checked for the
validity  of condition given in the chapter-3 of manual, from this  I
understood that the generated box obeying all the conditions except the one
in 3.3 i.e |Cx| <=1/2ax . Here my doubt is what changes can I make to my
system in order to make it follow all the rules required for the reduced
basis  lattice without disturbing its  morphology as it is a crystal, that
means how can I rotate, orient  or align my system are there any built in
tools in GROMACS to achieve this and how would I get new box vectors and
angles after rotating/aligning to generate the box for modified system.

Thank you in advance.

Regards,
Ramesh.


On Thu, Sep 27, 2012 at 1:09 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.
> >
> >
> >
> > Thank you in advance,
> >
> > 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
> Canada
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