Re: Protein in/out of box

From: Gianluca Interlandi (
Date: Mon May 28 2007 - 10:33:29 CDT

Yes, this is normal. Please, see older NAMD list threads to unwrap the


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
                    +1 (206) 685 4435
                    +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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