VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Mon Apr 28 2003 - 12:07:46 CDT

Ioana,

On Fri, Apr 25, 2003 at 01:34:41PM -0700, Ioana Cozmuta wrote:
> Hi John,
>
> I have a question related to unit cell parameters values. When I load a
> pdb file and then a .dcd trajectory corresponding to some NPT dynamics is
> there a way to monitor in VMD the unit cell parameters and retrieve the
> values at each step? Or at least for a fixed frame what is the way to get
> the values of the UC parameters? Do you happen to know what is the way to
> output the values for the UC during dynamics in NAMD?

It's possible in principle to parse the .xst file output in NAMD to load
the unit cell data into VMD through a Tcl script; the hardest part will
probably be to match lines in the .xst file with frames in the dcd file.

Alternatively, the lastest versions of NAMD (probably unreleased at this
point) have a new option called "dcdUnitCell" which will store unit cell
data in the dcd file. This info will be automatically read by VMD if it
detects it. Note that using this NAMD option will produce a dcd file that
cannot be read by x-plor.

Cheers,
Justin

>
> Thanks in advance,
> Ioana 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys