Dear all,
For MD we need to get a initial velocity of the molecule randomly. Id the
velocity linear vvelocity of the whole molecule or the vibration velovcity or
some kinds of other velocity?
In addition, as for the molecule is very large, there is the possibility that
differeny parts of the protein has different velocity. Does this violate the
randomly got velocity?
Further more, for the MD system. it is in fact protein (can include ions and
ligands) surrounded by water. Then it seems there will be no linaear movement
of the whole molecule.
I am looking forward to having these clarified.
Best regards.
Fenghui Fan
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