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 <[email protected]> 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 <[email protected]> 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 <[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 >> > -- > 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
