Tutorial-l Mailing List

From: Timothy Isgro (timisgro_at_ks.uiuc.edu)
Date: Fri Feb 16 2007 - 11:56:48 CST

Hi Sap,

If you would like to simply analyze the data that you already have
(as opposed to measuring the COM velocity on the fly in NAMD), you
can use VMD to do this. Assuming you have the coordinate data along
with your velocity data, I would simply load the system in VMD, and
invoke the "measure center" command with "weight mass" to measure the
COM of your atom selection at each step in the trajectory. With the
position of the COM at each step and the length of the time step, the
velocity is simple to calculate. A short tcl script will do this for
you.

-Tim

On Feb 6, 2007, at 6:05 PM, saravana wrote:

> Dear users
>
> Is there any option in namd for calculating centre of mass
> velocity ? i have a
> velocity trajectory file for 5ns
>
> thanks in advance.
>
> sap
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