Re: [AMBER] center of mass motion

From: Daniel Sindhikara <>
Date: Fri, 18 Feb 2011 11:57:33 +0900

As far as I know, you can't directly output the center of mass trajectory.
Thus, there are three options I can think of:
1) Pick an atom that stays near the center of the (protein?) and print out
that trajectory.
2) Use ptraj to trajout the protein only using a mask, then make your own
program to analyze the com of the coordinates.
3) Do you need to know the full trajectory? Usually people care more about
the distance along the vector normal to the membrane. In this case, look up
the vector command in ptraj in the ambertools manual.


On Thu, Feb 17, 2011 at 10:09 PM, siddesh southekal <
> wrote:

> Hello all,
> I have a system containing protein, lipids and solvent
> I want to compute the motion of center of mass along the simulation
> trajectory of the protein.
> Is this possible using ptraj ? Can anybody give me an idea how i can do
> this
> ?
> sid
> _______________________________________________
> AMBER mailing list

Dr. Daniel J. Sindhikara
Institute for Molecular Science
AMBER mailing list
Received on Thu Feb 17 2011 - 19:00:02 PST
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