Re: Protein in/out of box

From: Peter Freddolino (
Date: Mon May 28 2007 - 08:50:17 CDT

Hi Monika,
please have a look in the namd-l archives for other threads with this
question, such as the discussion rooted at In
brief, this doesn't indicate that your results are unreliable; it's just
that part (but not all) of your protein has moved into the periodic
image of your solvent box, but the output coordinates will not be
wrapped unless a complete chain of covalently bonded atoms move. If
you're only concerned with the protein, simply aligning the frames
should be fine for most of your analysis. You can also have a look at
the pbctools plugin
( for manipulating
this. Please note that this is *not* a "discrepancy"; this is exactly
how the output is supposed to behave.

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....
> ===========================

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