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 <[email protected]> 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. > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
