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

Sun Oct 14 09:21:45 CEST 2012

Dear  Tsjerk,

                       Thank you for your valuable suggestions, I have done
as you have suggested,  by doing so my simulation cell has satisfied all
the conditions required for the reduced basis lattice but now lattice
parameter beta has again changed to 102 degrees which was initially taken
as 125.4 degrees as provided by crystallographers.
 Is there a way so that I can continue my simulations in Gromacs with the
lattice parameters provided by crystallographers as I am intending to
measure how lattice parameters vary with temperature and compare them with
the experimental results.
Now, I am unable to compare my lattice parameters with experimental values
as  Gromacs is changing the simulation cell to its convenient way (beta
starting from 102 degrees originally should be 125.4 degrees ).

Thank you in advance,

Regards,
Ramesh.

On Wed, Oct 10, 2012 at 4:51 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Ramesh,
>
> You already got a good handle on it! You can subtract and add vectors
> without changing the lattice. Now, the box in gromacs will be
> something like ((ax, 0, 0), (bx,by,0),(cx,cy,cz)). If cx > 0.5*ax,
> then you can change the vector to (cx-ax,cy-0,cz-0), and the new |cx'|
> will always be smaller than ax.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Oct 10, 2012 at 11:47 AM, ramesh cheerla
> <rameshgromacs at gmail.com> wrote:
> > 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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>
> --
> 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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