AMBER Archive (2008)

Subject: Re: AMBER: Origin of periodic box

From: Gustavo Seabra (
Date: Thu Oct 16 2008 - 08:24:50 CDT

On Wed, Oct 15, 2008 at 9:34 PM, Naser Alijabbari wrote:
> I was wondering what the origin (0,0,0 = x,y,z) is for the above coordinates
> or how are the coordinates assigned for each atom (I am guessing it can't be
> the center of my box because then my 26.5 would be my largest coordinate,
> and I would also have negative coordinate values which I don't see.)

I've been bit by this before :-)

AFAIK, the origin of coordinates in Amber is on one corner of the box.
If you load the system in VMD, for example, that would show as the
lower-left-front corner.

> Also I tried using the below commands to create a new restart file:
> trajin bbprotein5.rst
> center :1-108
> image center familiar
> trajout bbproteincntrd.rst restart
> I thought this would only affect my coordinates but looking at the new
> restart file my velocities are all zeroed. Can someone explain why?

This is not an "amber" problem, but a known ptraj "feature". Basically
it only deals with the coordinates and what it gives you is not
exactly a new restart file, but would probably be better described as
a new file with the coordinates in "restart" format. It does not
prints the velocities, and puts zeroes for all of them.

If you want the velocities, what you can do is to copy them from the
original restart file into the new (wrapped) one, since the velocities
should not be affected by wrapping.

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