AMBER Archive (2006)

Subject: RE: AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 23 2006 - 06:34:47 CDT

Hi Ricardo,

> I am using a truncated octehedral TIP3P type water box in my
> simulations using
> PMEMD with AMBER8, however when I try to center and reimage
> the system using
> the common keywords:
>
> center mass
> image center
>
> I got a new trajectory with a distorted cubic shape in which
> the solute is
> partialy out of the box and not in the center as I expected!
>
> What should I do to overcome this problem?

What you are seeing is the triclinic unit cell which is how a truncated
octahedron is actually treated and replicated inside sander. If you add the
keyword 'familiar' to the image line of your ptraj script then it will get
translated back into the truncated octahedron shape you are familiar with.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| 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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