velocity.pdb and velocity unit in NAMD

From: Kowsar Khajeh (
Date: Tue Jul 24 2018 - 01:07:13 CDT

Hello all NAMD users
I have read below posts about the unit of velocity in NAMD files (different
I tried to simulate the motion of one atom in specific direction. I have
prepared the *input.pdb* as a input velocity in my simulation. I have set
the initial velocity *V=(0, 4165.58, 0)* in below comment in the
*inputvelocity.pdb* file and called it in the config file same as below;
*velocities **inputvelocity.pdb*
in my configuration file, I have set below comment to see the final
velocity of the atom;

*binaryoutput nobinaryrestart no*
Since the only one atom exists in the box (there is no effect from bonded
and nonbonded interaction) so I can see the motion of atom in *"Y"*
direction at constant speed.
After finishing the simulation I have opened the "file.vel" and saw that
the velocity is (0,165.58, 0).
My question is that; what is the effect of "inputvelocity.pdb".
Thank you in advance

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