AMBER Archive (2002)

Subject: Re: amber trajectory

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Wed Dec 18 2002 - 09:02:05 CST

Hi, Ioana,
    You may try to remove the box information from your explicit solvent
trajectory or choose the proper option in VMD to view this kind of
trajectories. I know the new version has this feature.

On Wed, 2002-12-18 at 00:16, Ioana Cozmuta wrote:
> Hi amber-users,
>
> I have a small trajectory generated with amber7 on SGI/IRIX (octane)
> machine. It is a cubical water box (L=20A) and I've run NVT dynamics
> using PBC. When I load the .crd file into VMD the bonds seem to be
> extremely stretched. However from the output it seems that there is
> nothing really wrong with the energy or with the run itself. I wonder if
> this is an artifact of the PBC visualisation in VMD?
>
> Thank you and Happy holidays!
>
> Ioana
>
>
> ****************************************************************************
> * Ioana Cozmuta, PhD * *
> * NASA-AMES Research Center * "Gravitation can not be held responsible*
> * Mail Stop 230-3 * for people falling in love" *
> * Moffet Field,CA 94035 * *
> * phone: (650) 604-0993 * Albert Einstein*
> * fax: (650) 604-0350 * (1879-1955) *
> **************************************************************************** 

-- 
Guanglei Cui <cuigl_at_morita.chem.sunysb.edu>
SUNY at Stony Brook