VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 01 2011 - 20:15:06 CDT

On Sun, May 1, 2011 at 8:29 PM, B.M.B. Vanschouwen
<vanschbm_at_univmail.cis.mcmaster.ca> wrote:
> Hello.
>
> 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?

whatever you do, it will at best be a crude approximation.

whether using only the oxygen atoms or all atoms is the better
solution, depends on whether they are wrapped on a per-atom
or per-molecule basis. using only oxygens is likely to be the safer
option, with a tendency to underestimate the dimensions.

cheers,
     axel.
it will error on the small side.

> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.