Protein in/out of box

From: Monika Sharma (
Date: Mon May 28 2007 - 06:10:43 CDT

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

Life is all about exploration....

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