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

[Tsjerk Wassenaar]

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