From: B.M.B. Vanschouwen (
Date: Sun May 01 2011 - 19:29:03 CDT


I am trying to reconstruct a lost XST file from a corresponding DCD
file (using a Fortran script, and for use in a subsequent Fortran
analysis). The DCD file does not have unit cell parameters, so I am
trying to measure the periodic box dimensions from the solvent box (in
which the water molecules have been wrapped around the periodic
boundaries), following a logic similar to that used to set the initial
box dimensions during simulation set-up (for NAMD).

Are there any special considerations for this method? For instance,
should I compute the box dimensions based on coordinates of all water
atoms, or just the water oxygen atoms?