On 21/06/2011 3:43 PM, Kavyashree M wrote:
Sir,
I am extremely sorry for this question again :(
but I wanted to know this violation exists only in
first 50ns but after that even though there appears
to be a point of violation its only 1.39nm which is
o0.01nm less than the cut off which I hope does
not cause serious trouble (as the minimum bond
length is of the order of 1 Angs) So can I make use
of this part of trajectory?
The purpose of the minimum image convention is to help model the real
conditions under which your protein exists. The usual case is one of
(effectively) infinite dilution. However, if you have a protein atom
that is influenced by an atom of a periodic image of the protein, then
you are not close to modeling infinite dilution. Arguably, a water atom
that can see two different periodic images is also unrealistic, but
probably this will be a lower-order effect, and vary from case to case.
So as soon as you get a violation, further data about your system is
tainted from the previous existence of unrealistic conditions. Even just
looking at the first part of the simulation before the violation
(assuming it has equilibrated properly so far) is questionable, because
you have imposed on its ensemble the restriction that it cannot grow
larger than a given diameter for a given orientation. It's up to you to
judge whether the effect is small enough to ignore, and that depends on
lots of things we can't know.
There exist a large number of areas of biomolecular simulations where
our inability to exhaustively sample ensembles has limited our ability
to quantify the size of various effects. The effect of violations of
minimum-image conventions on proteins is one of those areas.
The important lesson here is that doing a simulation blindly runs a
large risk of wasting resources. Ongoing attention to lots of details is
important. As in many fields of human endeavour, there are lots of
lessons that have been written in the blood of unfortunate people before
you. In research, there will be lessons written in your blood. The trick
is to learn from the former in order to minimize the latter :-)
Mark
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