Hello Justin, THanks for your reply.
Suppose any atom that leaves a simulation box by, say, the right-hand face, then enters the simulation box by the left-hand face. For these atom how gromacs save the coordinate. Does it save the coordinate when it enter from left-hand face? Nilesh On Wed, April 13, 2011 9:26 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> >> If some part of molecule is outside the box. How Gromacs save the >> coordinates in trajectory. >> > > There is no such thing as "outside" in a periodic system. > > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condit > ions > > -Justin > > >> >> Nilesh >> >> >> >> > > -- > ======================================== > > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
