VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jul 26 2007 - 11:50:43 CDT

On Thu, 26 Jul 2007, sally cii wrote:

hi rachel (or sally??)

SC> Hi, Olaf
SC>
SC> Thank you for your reply. When I loaded the AMBER parm file (which should
SC> contain box information) and then trajectories into VMD, by default VMD

the box information from the .parm file (if there is any) will not be
used by VMD. it only reads box dimensions along the trajectory from
the coordinate files (it is a per-step property and .parm files do
not contain any coordinates).

SC> draws a rectangular box for that trajectory, can I ask how does VMD makes
SC> this box? and if I use this rectangular box rather than the original

can you please explain how you generate that box?
by default VMD does nothing like that without you
calling some other script that draws a box.

cheers,
   axel.

SC> truncated octahedral box to wrap the trajectory, how would that change the
SC> trajectories?
SC>
SC> Best regards,
SC> Rachel
SC>
SC>
SC> On 7/25/07, Olaf Lenz <olenz_at_fias.uni-frankfurt.de> wrote:
SC> >
SC> > -----BEGIN PGP SIGNED MESSAGE-----
SC> > Hash: RIPEMD160
SC> >
SC> > Hi!
SC> >
SC> > Rachel wrote:
SC> > > Can anyone tell me how to wrap the trajecotries into a truncated
SC> > > octahedral box? thank you for your help.
SC> >
SC> > The pbctools so far are only able to wrap into a parallelepiped or the
SC> > corresponding rectangular box. Truncated octahedrons are not supported,
SC> > yet. You would be very welcome to extend the pbctools plugin!
SC> >
SC> > Olaf
SC> >
SC> > -----BEGIN PGP SIGNATURE-----
SC> > Version: GnuPG v1.4.2 (GNU/Linux)
SC> > Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org
SC> >
SC> > iD8DBQFGp4rbtQ3riQ3oo/oRA9k6AJ9XgJU9KRS2WD6REfh83NcnsU9iwACgkHtn
SC> > h7lSV6fCi7Lft6VjaqWlyu0=
SC> > =2xxy
SC> > -----END PGP SIGNATURE-----
SC> >
SC> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.