periodic boundary condition in CHARMM

[Niharendu.Choudhury-.at.-mail.uh.edu]

Hi ccl-users
 I am a new CHARMM user.
 In CHARMM (version c26b1) for liquid water simulation  with PERIODIC BOUNDARY
 CONDITION in a cubic box with box length say 31.063 angstorm, if i use the
 following command is that okay.
 command i used:
 Crystal Define Cubic  31.063 31.063  90.0 90.0 90.0
 Crystal Build noperations 0
 Do the above  commads mean coordinates of all the particles, those are out of
 the primary box, in EVERY dynamic TIME STEP will be set back in the primary
 simulation box?
 If so, then in my final output coordinate file, I found some coordinates which
 are outside the box, say -20.5 and 20.05 etc.
 Please explain.
 Nihar