Re: [gmx-users] saving coordinates

Hey :) With domain decomposition the particles are saved with the coordinates corresponding to the position in the rectangular brick with sides equal to the diagonal elements of your unit cell. With particle decomposition the positions are taken for which holds that the first atom of the molecule

Re: [gmx-users] saving coordinates

Nilesh Dhumal wrote: 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

Re: [gmx-users] saving coordinates

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, A

Re: [gmx-users] saving coordinates

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_Conditions -Justin Nilesh -- =