Tsjerk, your good reference helped me to understand the set_pbc and pbc_dx functions from g_dist... I changed few lines of it and my problem was solved. Thank you.
Cheers. Fernando. 2009/4/14 Tsjerk Wassenaar <tsje...@gmail.com> > Hi Fernando, > > Just bear in mind that these lattice vectors are just translation > vectors. You can add them to or subtract them from the positional > vectors of the com. That way you'll get a number of points which you > can use to calculate the distances the regular way. To see where you > went wrong, consider that a vector of the triclinic unit cell may have > more than one non-zero component. You considered only one non-zero > component, based upon the rectangular brick representation. But from > Pythagoras theorem it follows that doing so will make you miss part of > the true distance and come to an underestimate of it. > There is a niftier solution to the smallest distance, which will work > regardless of the separation between particles/coms in the infinite > system. It's in my thesis (Chapter 3, Appendix C, page 68): > > http://dissertations.ub.rug.nl/faculties/science/2006/t.a.wassenaar/?FullItemRecord=ON > > Hope it helps, > > Tsjerk > > On 4/14/09, Fernando C <fernando.cesar...@gmail.com> wrote: > > Hi Tsjerk and all list! > > > > > You have to use the three vectors from the tricilinic representation > > > to obtain the correct distance in the periodic system. Check PBC in > > > Chapter 3 of the manual. > > > > > > I used the length values from rectangular box because I'd want believe > that > > my problem would be solved easily; I wouldn't want to fall in question of > > calculate positions and distances in triclinic cells. But here I am: > could > > anybody explain to me the algorithm of how such things are calculated? > > > > Thanks again! > > > > Fernando. > > > > > > > > > > > > -- > > And Noel Gallagher said: Gromacs is gonna live forever! > > > > 2009/4/13 Tsjerk Wassenaar <tsje...@gmail.com> > > > > > > Hi Fernando, > > > > > > > > > > I've obtained the vectors for the rectangular box in g_energy, > > > > using Box_XX, Box_YY and Box_ZZ options; I didn't use the vectors of > the > > > > skewed box.) > > > > > > You have to use the three vectors from the tricilinic representation > > > to obtain the correct distance in the periodic system. Check PBC in > > > Chapter 3 of the manual. > > > > > > Cheers, > > > > > > Tsjerk > > > > > > -- > > > Tsjerk A. Wassenaar, Ph.D. > > > Junior UD (post-doc) > > > Biomolecular NMR, Bijvoet Center > > > Utrecht University > > > Padualaan 8 > > > 3584 CH Utrecht > > > The Netherlands > > > P: +31-30-2539931 > > > F: +31-30-2537623 > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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