VMD-L Mailing List

From: lan hoa Trinh (trinhlanhoa_at_gmail.com)
Date: Thu Aug 31 2017 - 17:51:12 CDT

Dear John,
Thank you. The unit is nm. I intended to use the big box.

*Lan Hoa*

2017-08-31 17:34 GMT-05:00 John Stone <johns_at_ks.uiuc.edu>:

> 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/
>