From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon May 28 2007 - 10:45:29 CDT
Actually, you don't need to unwrap the coordinates if you only have to
calculate things like the root mean square deviation (RMSD) and you have
only one protein in your system. It is enough to align your protein with
the first frame along your simulation. How to rms align a protein with VMD
is described in:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node185.html
and the subsections linked there.
Hope this helped,
Gianluca
On Mon, 28 May 2007, Gianluca Interlandi wrote:
> Yes, this is normal. Please, see older NAMD list threads to unwrap the
> coordinates:
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5714.html
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5716.html
>
> Gianluca
>
> On Mon, 28 May 2007, Monika Sharma wrote:
>
> > Dear All,
> > I am doing 10ns simulation (production run) of a small protein. The run as
> > such seems to be going fine. But when I am viewing the dcd file in VMD, it
> > seems that the protein tries to diffuse out of the solvent box. A good portion
> > of it can be seen out of the box, and then it moving from one edge of the box
> > to other, and then wrapping back. The trajectory looks so weird that the
> > protein goes out from one edge; move to another edge in next frame, then again
> > come back to the former edge and wrapped back. It can be seen happening 3-4
> > times during 10 ns run. Now my question is that ; Does it indicate that
> > results are not reliable (because then i may be looking for rmsd and rgyr
> > plots which will depend upon the alignment of the frames), or is it a routine
> > thing that happens with longer simulations and i can go ahead with my
> > results?? (because this is the longest simulation I have given till now). or
> > Can there be any option to remove these discrepancies in the run? I am using
> > wrapAll on, wrapNearest on in the conf file. If anybody can help me out...
> > Thanks in advance
> > Regards,
> > Monika
> >
> > ===========================
> > Life is all about exploration....
> > ===========================
> >
>
> -----------------------------------------------------
> 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.
> -----------------------------------------------------
>
-----------------------------------------------------
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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