Alignment of velocity dcd file

From: Mert Gür (
Date: Sat Aug 22 2009 - 15:03:10 CDT

Dear all,
Lets say that I have a coordinate dcd file "dcd1" and a velocity dcd file
"vel1" both of size 2000x1200.
I align my protein using vmd and save the aligned coordinates as "dcd2".
Now I can easily obtain an rotation matrix rot of size 2000x2000 that
performes the following transition


What I want to do is to eliminate the terms in the velocity due to
transition and rotation of my protein. Does the following transition make
sense in that light?


I am asking because the velocities seem to increase if I do this matrix
multiplication. Since I am eliminating some of its components, the
velocities should actually decrease.
So at that point I started to doubt if the velocities due to transition and
rotation are included in the velocity dcd file?

The manual just says

*Description: * The binary DCD velocity trajectory filename. This file
stores the trajectory of all atom velocities using the same format (binary
DCD) as X-PLOR. If velDCDfile is defined, then velDCDfreq must also be

Can anybody help me out with that?


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