VMD-L Mailing List

From: Èùìáò Åõáããåëéäçò (te8624_at_mbg.duth.gr)
Date: Sat Jul 14 2007 - 11:32:17 CDT

Hello,
I have the same problem, it returns a=b=c=1.00 and alpha=beta=gamma=90.00. The
VMD version that I use is the latest but I don't know the origin of the dcd and
psf files that I am using.
Is there a way to estimate the unit-cell dimensions, which is more precise than
this:

measure minmax [atomselect top all] ?

What about the alpha,beta and gamma angles?
I thank you in advance,

Thomas Evangelidis

Hi,
  This tells me two things:
1) You're using loading the DCD with one of the older versions of VMD
   (which defaulted side lengths to 1.0, new version defaults to 0.0)

2) Your DCD trajectory was written by an older version of NAMD that didn't
   save periodic cell information in the DCD file.

It would be helpful to know the precise version of NAMD you're running,
since that'll tell me much more about the particular DCD style you're
working with. (the NAMD DCD output has changed a few times over the years...)

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 03, 2006 at 07:04:48PM +0000, ziemys_at_ecr6.ohio-state.edu wrote:
> Hi,
>
> When I apply "molinfo top get {a b c} fram ..." in tcl, i got the length equal
to 1.00. I have used to load NAMD output DCD with PSF.
>
> Why the cell length are missing ?
>
> With best
> Arturas Z.
>