VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Jul 14 2007 - 11:42:08 CDT

On Sat, 14 Jul 2007, [iso-8859-7] Θωμας [iso-8859-7] Ευαγγελιδης wrote:

TE> Hello,
TE> I have the same problem, it returns a=b=c=1.00 and alpha=beta=gamma=90.00. The
TE> VMD version that I use is the latest but I don't know the origin of the dcd and
TE> psf files that I am using.

thomas,

the psf has no information about the cell dimensions (or any
other geometry information).

the dcd file, however could have been created with VMD or CatDCD.
nevertheless, the unitcell information is evidently lost.

TE> Is there a way to estimate the unit-cell dimensions, which is more precise than
TE> this:
TE>
TE> measure minmax [atomselect top all] ?

not really. i would look into the directory where the
trajectory data is stored, whether there are other files
containing the cell information (e.g. .xst) which can
be read in and applied to a trajectory with the PBCtools
plugin.
 
TE> What about the alpha,beta and gamma angles?

same thing. one could think about coming up with
a minimization scheme, that optimzes the cell parameters
to yield the expected density and minimize energy,
but by the time this works correctly, you probably
have redone that simulation a couple of times and then
you have the parameters accurately.

cheers,
   axel.

TE> I thank you in advance,
TE>
TE> Thomas Evangelidis
TE>
TE>
TE>
TE> Hi,
TE> This tells me two things:
TE> 1) You're using loading the DCD with one of the older versions of VMD
TE> (which defaulted side lengths to 1.0, new version defaults to 0.0)
TE>
TE> 2) Your DCD trajectory was written by an older version of NAMD that didn't
TE> save periodic cell information in the DCD file.
TE>
TE> It would be helpful to know the precise version of NAMD you're running,
TE> since that'll tell me much more about the particular DCD style you're
TE> working with. (the NAMD DCD output has changed a few times over the years...)
TE>
TE> John Stone
TE> vmd_at_ks.uiuc.edu
TE>
TE> On Wed, May 03, 2006 at 07:04:48PM +0000, ziemys_at_ecr6.ohio-state.edu wrote:
TE> > Hi,
TE> >
TE> > When I apply "molinfo top get {a b c} fram ..." in tcl, i got the length equal
TE> to 1.00. I have used to load NAMD output DCD with PSF.
TE> >
TE> > Why the cell length are missing ?
TE> >
TE> > With best
TE> > Arturas Z.
TE> >
TE> 

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.