From: Axel Kohlmeyer (
Date: Tue Apr 26 2011 - 11:31:28 CDT

On Tue, 2011-04-26 at 11:02 -0500, John Stone wrote:
> Hi,
> There's not an existing tool to do this, and I'm not sure that the
> associated DCD file and NAMD console output contain enough information
> to recreate the lost .xsc file. If the data in the .xsc was redundant


the .xsc file in addition contains information about the origin
that is not available in a dcd file or VMD.

this is the reason why the pbctools have to have a -origin flag.
for a periodic simulation the origin is mostly unimportant, but...


> vs. what's the in DCD file, the .xsc file wouldn't be needed in the first
> place.... This question is best asked on the NAMD-L list however, as
> the details of your simulation probably matter and either
> Jim or the other NAMD experts would know better than I do.
> Cheers,
> John Stone
> On Wed, Apr 20, 2011 at 05:36:04PM +0530, Neelanjana Sengupta wrote:
> > Dear VMD experts,
> >
> > While running my simulations with NAMD (mostly with rectangular periodic
> > boundary conditions), I write out .dcd trajectories that contain the unit
> > cell information. I usually do not save an .xst file. However, in
> > principle, I can write out a file in the format of the corresponding .xst
> > file.
> >
> > If (say accidentally) I lose the .xsc file, is there a tool/plugin which
> > will allow me to generate the .xsc file again, if I am able to provide the
> > periodic cell parameters?
> >
> > Thanks in advance,
> > Neelanjana Sengupta

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.