VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Wed Jan 08 2020 - 04:41:12 CST

Awesome, thanks!

On Wed, Jan 8, 2020 at 5:33 AM Christian Seitz <cseitz_at_ucsd.edu> wrote:

> 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>
> 

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*