Re: query about wrapped coordinates

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri May 04 2007 - 14:54:20 CDT

> I have been doing a periodic NVE run of my protein in solvent.
> I had the "wrap all" command on during the run. Some part of my protein
> which moved out of box has been wrapped back but i want to know the
> coordinates of my protein corresponding to the one when it was moving in
> one direction. I also want to fit the different frames to first one in
> such a way that i dont observe the half portion of protein moving on
> other side. ANy suggestion are highly appreciated from more experienced
> users.

Hi Harish,

I forward you here the response I got from Jerome when I posted the same
question on the NAMD list a year ago.

Best,

   Gianluca

---------- Forwarded message ----------
Date: Thu, 5 Oct 2006 23:08:18 -0400
From: Jerome Henin <jhenin_at_vitae.cmm.upenn.edu>
To: Gianluca Interlandi <gianluca_at_u.washington.edu>
Cc: <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: "wrapAll on" with a complex

Gianluca:
Using VMD with the attached script should solve that. Just source the Tcl file
and use the 'unwrap' procedure.
Best,
Jerome

Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :
> I am performing a simulation of a complex consisting of two proteins. I am
> using the option "wrapAll on". One of the two proteins has reached one of
> the boundaries of the box and it has been wrapped around. The other
> protein is still in the same position.
>
> Is there a way to "recover" from the wrapping a posteriori, i.e., to bring
> the protein back to its original image?
>
> Thanks a lot,
>
> Gianluca
>
> -----------------------------------------------------
> Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://biocroma.unizh.ch/gianluca/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

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