VMD-L Mailing List

From: Christian Seitz (cseitz_at_ucsd.edu)
Date: Tue Jan 07 2020 - 17:37:24 CST

Hi John,

Thanks for the suggestion! I hadn't thought of that before. Indeed, the
first frame of my trajectory had no PBC parameters, but the rest did. For
future readers, here is how I wrapped my trajectory:

(at frame 0) % molinfo top get frame #this tells you what frame you're on
(at frame 0) % set cell [pbc get -now] #this tells you what are the PBC
boundaries for the frame you're at, showing that there are no boundaries at
this frame for my system
(at frame 1) % set cell [pbc get -now] #find PBC parameters
(at frame 0) % pbc set {x1 y1 z1 x2 y2 z2} #where x1-z2 are the PBC
parameters from the command above
(at frame 0) % pbc wrap -compound fragment -center com -centersel "segname
PROA" -all

Note, using -compound residue left my trajectory with a few molecules in a
different frame, and excessively long bonds in between them. I used segname
PROA because this chain was not flipping during any trajectory.

Best,
Christian

On Tue, Jan 7, 2020 at 12:27 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
> 

-- 
*Christian Seitz*
PhD Student, Biochemistry & Biophysics | UC-San Diego
NSF GRFP Fellow, Amgen Scholar
McCammon lab <https://mccammon.ucsd.edu/> and Amaro lab
<https://amarolab.ucsd.edu/>
cseitz_at_ucsd.edu <cseitz_at_elon.edu>
[image: www.linkedin.com/in/christianseitz21]
<http://www.linkedin.com/in/christianseitz21>