> By random rotation, I mean the rotation that I observed happens too quick to
> be true. In my opinion, the time scale of the rotation should be around 1 ns
> or more. But the rotation in my case just happen within a couple of 100 fs.
> Please check the animation from links in my very first mail.
The animations are not clear to me and I cannot tell what processing you
have done to obtain the images. If it is an imaging issue, you should see
molecules moving outside the periodic box or abruptly translating (the box
length) not rotations.
If the polymer is one single molecule (i.e. residues 1-125) then it is
definately not an imaging issue (since molecules are imaged intact).
I would run the trajectory with IWRAP=0 dumping out every step (NTWX = 1)
or every 5 steps in a (short) 5 ps run (since you claim you are seeing
funny motion on 100 fs time scale). If in the continuous dynamics you see
funny stuff, this is probably a force field issue with your polymer and
not an imaging issue.
With IWRAP=0 if molecules are moving out of the box you will see
molecules continuously move further and further from the central box. If
so, this is potentially imaging. If not, then it has nothing to do with
RMS or IMAGE.
I would look at a movie of the chain of carbon atoms (with the water
hidden) or a movie of a subset of the polymer. If you dump every frame,
you should not see abrupt motions (except via box translations, however,
these will be absent with IWRAP=0).
--tec3
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Received on Thu Aug 25 2011 - 14:00:03 PDT
