[gmx-users] Intial velocity

[Fan, Fenghui]

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