Jan17-13, 12:42 AM
I wish to get some explanation on calculating velocity auto-correlation for water molecules in a box.
I have done 100 ns molecular dynamics simulation on 1445 water molecules in a box. Also I have calculated velocity for each water molecule in a frame. A frame contains 1445 water molecules, so for each frame I have 1445 velocity values. I have total 10000 frames.
Now I want to calculate the velocity auto-correlation function for this system. I am confused if I shall need to calculate average velocity for each frame (average for 1445 molecules in one frame) - this means I will have 10000 averaged velocities, each value will represent velocity from each frame (total 10000 frames).
And then calculate the velocity auto-correlation function?
I appreciate any explanation.
Thanks in advance.
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