AMBER Archive (2009)

Subject: RE: [AMBER] ptraj "image" "center" commands

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jun 11 2009 - 10:30:08 CDT

Hi Catein,

> I have some problem with the use of ptraj for mdcrd files analysis.
>
> What does it mean by image?

This reimages the waters back in to the central simulation box since by
default sander writes the coordinates of the original atoms even as they
translate into adjacent boxes. See section 5.2.4 of the first tutorial for
an explanation.

http://ambermd.org/tutorials/basic/tutorial1/section5.htm

 
> Why we need center?

Dealers choice. It can just make viewing things easier. The center command
just moved the origin of the box to a specific location which can make it
easier to see what is going on when you look at the trajectory.
 
> Does these two commands "image" or "center" needed when we want to
> generate rmsd, average structure, correlated motion and fluctuation
> results only?

These commands are not required, they are there effectively to make
visualization easier. The exception is if you are trying to calculate water
RMSD etc since without the imaging it will just keep steadily increasing. It
does not hurt to run these commands so in general I find it best to include
them.

All the best
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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