On 24/11/10 02:47, Mark Abraham wrote:
On 24/11/2010 5:04 AM, ms wrote:
On 23/11/10 17:00, Mark Abraham wrote:
There is no general solution for bonds visualized on a
single set of coordinates, however - over a trajectory, either molecules
appear to diffuse out of the box, or appear to break.
Yep, but if they appear broken because they are at the pbc boundaries
is no big deal. The problem (and with this I answer also Florian
Dommert) is that using -pbc tends to "break" stuff *inside* the box.
That can't be true in general. Use of one of the five different -pbc
options, possibly with -center and -ur, possibly over several
invocations has always worked for anything I've wanted. However it's
hard to answer an assertion that something is broken if you don't know
what the person has tried :-)
You are absolutely right, but well, it was not needed for the aestethic
purposes so far required :)
Of course if and when needed for analysis, I'll try harder with trjconv
-pbc arcanes.
thanks!
m.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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