VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 07 2020 - 14:27:38 CST

Hi,
  It sounds to me like some of your trajectory files contain frames
that have PBC side lengths of zero. You can check this in VMD itself
after loading frames by querying them with:
  molinfo top get frame
  molinfo top get {a b c alpha beta gamma}

You can similarly inspect any arbitrary frame's information...

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jan 06, 2020 at 04:37:42PM -0800, Christian Seitz wrote:
> Hello,
> I have been running a long NAMD simulation of a homotetramer protein in 12
> chunks. A few months ago I finished the first 6 chunks; one monomer of the
> tetramer would flip to a different box during some chunks. So I combined
> those trajectories into a single trajectory and wrapped it using the TK
> Console with:
> pbc wrap -centersel "protein" -center com -compound residue -all
> pbc unwrap -first now
> Now, I've finished all 12 chunks of the simulation and again combined the
> chunks of trajectories into a long one. But now, I cannot wrap the full
> trajectory or any of the shorter chunks anymore, and the pbc boundaries
> get deleted. For example, directly after loading a trajectory:
> % set cell [pbc get -now]
> {169.186295 169.186295 226.764709 90.000000 90.000000 90.000000}
> % pbc wrap -centersel "protein" -center com -compound residue -all
> ERROR) Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000). Have
> you forgotten to set the pbc parameters?
> domain error: argument not in valid range
> % set cell [pbc get -now]
> {0.000000 0.000000 0.000000 90.000000 90.000000 90.000000}
> This happens regardless of the wrap commands I use. I can reinstate the
> boundaries with pbc set, but I then cannot get wrapping to work properly
> (it takes hours and in the end has some atoms in a different box, even
> after unwrapping or using different wrap commands). I have scoured the VMD
> mailing list and other sites, and haven't found anybody else with this
> problem. Any help would be greatly appreciated. Thanks!
> Best regards,
> Christian
> --
> Christian Seitz
> PhD Student, Biochemistry & Biophysics |Â UC-San Diego
> NSF GRFP Fellow, Amgen Scholar
> [1]McCammon lab and [2]Amaro lab
> [3]cseitz_at_ucsd.edu
> [4]www.linkedin.com/in/christianseitz21
>
> References
>
> Visible links
> 1. https://mccammon.ucsd.edu/
> 2. https://amarolab.ucsd.edu/
> 3. mailto:cseitz_at_elon.edu
> 4. http://www.linkedin.com/in/christianseitz21 

-- 
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/