From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon May 28 2007 - 10:33:29 CDT
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.
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