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 <[email protected]> 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 <[email protected]> > > > > 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 [email protected] > > 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 [email protected]. > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
