On 10/11/10 22:28, Justin A. Lemkul wrote:
First, let me see if I understand it correctly. From your explanation
(and intuition), it seems that the issue is that "center of mass" in a
periodic environment is ambiguous -there are always (at least) two
alternate configurations that have the center of mass at the center of
the box any time, and -center doesn't necessarily choose the most
compact one (i.e. the one where the box center is closest on average
to atoms). So, for example, in a 1-D periodic environment, this:
... O|O O|O ...
is equivalent to this
| OO | OO ...
the center of mass between the O's being always at the center of the
box in both cases.
Correct.
But I don't see how choosing one residue could help -I mean, the
residues wander practically everywhere in the box during the
simulation and none of them is privileged ; I don't see why centering
only around one would be better. It could help if they were only two,
but we talk of eight objects here (and possibly many more in the
future)...
...now I see it: You mean that, since I force to center around one of
the objects, and if on average it should belong to the cluster, the
whole thing should be more often than not within the box?
That's it. Take, for example, peptides A, B, and C. Peptide A is a
nucleation point for B and C to attach. Conceivably, trjconv could
choose a "center" that involves C on one "side" of the box and A+B on
the other. The whole protein is still "centered" by its criteria.
If, physically, A is in the core of the aggregate, then I could choose
some residue in peptide A and choose to center about it. There is no
other alignment that trjconv can assign, other than to place that chosen
residue of peptide A right in the middle of your unit cell. It can't be
broken any other way.
It seems to work right this time! Beautiful trick. Thank you again so
much -if I could, I would give you a big hug. I am still a newbie with
molecular simulations (my Ph.D. was on experimental biophysics) and I
still fall into a lot of easy traps!
cheers,
M.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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