Peyman,
the protein moves because the c.o.m. motion wasn't subtracted during
the dynamics.
On Tuesday 01 July 2008 12:24, Fabio Affinito wrote:
I think if it moves, then there is something more basic wrong, do
you remove
your center of mass motion appropriately? is your box homogeneously
equilibrated? but if it does not move and it looks like as if it
moved, then
it's visual problem and not important! you could e.g. write
something to cut
the solvent molecules from one side and put them on the other side
with some
mapping dependant on your box type, if you would like to see your
molecule at
the center.
btw, self diffusion is the diffusion of one molecule through others
of its own
kind, not through other molecules, solvent or else. if there is no
chemical
potential ( ~concentration ) difference, no mass transfer would take
place.
Peyman
Fabio Affinito, PhD
SISSA/ISAS -Statistical and Biological Physics
Via Beirut, 4
34014 Trieste
ITALY
email: [EMAIL PROTECTED] phone:+39 040 3787 303 fax:+39 040 3787 528
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