Dear all, I am running some molecular dynamics simulations with siesta 2.0, and I have a few doubts as to some of the output I am obtaining. I am running a md for a box with one DTT molecule and 24 water molecules in a 12.32 x 12.32 x 12.32 Angstroms box.
As my simulation runs, I see that in the .ANI file some of the water molecules simply "run away" from the simulation box - one of the H atoms, for example, is at R=(-3.225361, 17.279596, 40.989686). That got me a bit concerned about the PBC in the MD for siesta. If they are being properly taken into account, shouldn't this be reflected in the output of the atomic coordinates? Marcos -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Condensed Matter and Statistical Physics Sector International Centre for Theoretical Physics Trieste, Italy -------- I have become so addicted to vi that I try to exit OpenOffice by typing :wq!
