Re: [AMBER] Imaging & centering

From: de Manzanos Guinot, Angela <>
Date: Tue, 2 Jun 2015 17:11:44 +0000

Thank you very much explanation,it was really useful. I will update AmberTools now. And also regarding Jason suggestion, autoimaging doesn't work with my system, as it tries to bring all the subunits close to the first one, so it doesn't give me the solution I am looking for.

Best wishes,
De: Daniel Roe []
Enviado: martes, 02 de junio de 2015 18:05
Para: AMBER Mailing List
Asunto: Re: [AMBER] Imaging & centering


On Tue, Jun 2, 2015 at 10:33 AM, Angela de Manzanos <> wrote:
> reasonable solution using cpptraj V15.01b is by centering first all the

Any particular reason you are using a development version of cpptraj?
15.01b is over a year old at this point. I recommend updating to the
AmberTools 15 official release, freely available here:

> I know have a question about the imaging step. Am I with this set of
> commands forcing the waters and Na+ in a location different from where
> they are during the simulation? And if not, will this really tell me how

No. Imaging is essentially a visual trick. When you run with periodic
boundary conditions using PME the system is effectively surrounded by an
infinite number of copies (or images) of itself. Typically during a
simulation with PBC we "wrap" the output coordinates so that 1) they don't
eventually overflow (less of a problem these days if you are using NetCDF
trajectories/restarts) and 2) molecules appear like they're fitting nicely
in a box. When you re-image you are just shifting the positions of the
molecules inside the box - the relative positions with respect to images
haven't changed. Take for example two molecules A and B in a (poorly drawn)

| A B |
| |

If I shift the system so that A is centered:

| A | B
| |

Now B is outside the unit cell boundaries, so we re-image:

| B A |
| |

The relative positions of A and B haven't changed (the minimum imaged
distance, which is what 'distance' calculates by default, will be the same)
- B is now just where it would be in that neighboring unit cell.

Imaging can be very confusing at first, so don't worry if it seems strange
at first. Checking out some of the resources Jason recommended will
probably help.


> many waters are close to my ligand during the simulation or I am just
> forcing the waters to be in the periodic box?
> I am unsure about how the imaging command works and I am struggling to
> find information about it, so any help on this matter would be very much
> appreciated.
> Best,
> Angela
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jun 02 2015 - 10:30:04 PDT
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