suppose I am not going to use PBC and want all the atoms within the specified boundaries..
On Fri, May 14, 2010 at 1:42 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sikandar Mashayak wrote: > >> I have to create a box with given number of water molecules (spc/e) in it. >> So I use genbox -cs spc216.gro -maxsol n -box , with appropriate box size >> and n. >> But I observe in the out.gro that some atoms are outside the box, so How >> do I make genbox to keep all atoms within the box specified? >> >> > If you plan on using periodic boundary conditions, "outside" is > irrelevant... > > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > -Justin > > thanks >> sikandar >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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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