VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 31 2017 - 17:34:57 CDT

Hi,
  Best practice is to be sure to do "package require pbcutils" first.
VMD is getting the periodic cell information out of the Gromos
file reader plugin, but it looks to me like it has the wrong units:

molinfo top get {alpha beta gamma a b c}
90.000000 90.000000 90.000000 533.401489 533.401489 533.401489

If you zoom _way_ out, you'll see a box drawn there, but it's
far larger than the molecular structure that is displayed.

Even if I rescale the box side lengths down by a factor of 10,
I can still see that there's something wrong there with respect to
the size of the system vs. the size of the displayed periodic box:
molinfo top set {alpha beta gamma a b c} { 90 90 90 53.3401489 53.3401489 53.3401489 }

It looks to me like there's another factor of ~2 or so that remains
even after scaling down by a factor of 10. What length units were used
in that structure/simulation?

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 31, 2017 at 05:21:01PM -0500, lan hoa Trinh wrote:
> Hi ,
> I have a structure file, which is named as equil.gro (attached file).
> After visualizing the molecule with VMD, I type pbc box in Tk console but
> the box didn't show up.
> Plz help me to fix the bug. Thank you very much in advance.
> Best regards,
> Lan Hoa 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/