From: Jim Parker (
Date: Sat Dec 13 2014 - 15:02:17 CST

  Just closing the book on this. Bottom line was user error. I was using
a VMD tcl script to get the size of the box

    set meas [measure minmax $sel ]
    set x [expr { [lindex [lindex $meas 1] 0] - [lindex [lindex $meas 0] 0]
} ]
    set y [expr { [lindex [lindex $meas 1] 1] - [lindex [lindex $meas 0] 1]
} ]
    set z [expr { [lindex [lindex $meas 1] 2] - [lindex [lindex $meas 0] 2]
} ]

but in my simulations of the NPT ensemble usng NAMD and PBC, I had enabled
"wrapAll". The "wrapped" atoms generate a less dense overlap region that
is included in the measure minmax box size

If you use

 set cell [molinfo $molid get {a b c} frame $frame]

you will get the actual dimensions of the periodic cell, and an appropriate
volume and density.