AMBER Archive (2003)

Subject: Re: water box distortion

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Sat May 24 2003 - 20:26:21 CDT

GUILLERMINA L ESTIU wrote:
>
> I am not sure if I am fully understanding your solution. I can get back th water
> box, but ... wouldn't it get distirted again when equilibrating all the
> system... or during the simulation?

The "distortion" only appears when you look at the snapshots saved by
sander. Since you use periodic boundary conditions, during the
calculation, your central box is (virtually) replicated in all
directions to give a periodic array. This then means that a solvent
molecule leaving the central box is replaced by an image particle that
enters the box from the opposite direction. Hence, you don't have to
worry about this kind of "distortion".

Best regards

Holger

> On Fri, 23 May 2003 16:13:40, "David A. Case" wrote:
>
> > On Fri, May 23, 2003, GUILLERMINA L ESTIU wrote:
> >
> > > I am running simulations (amber 7) for a sistem of 2500 residuos (50000
> after
> > > building the water box)
> > > I am trying to equilibrate the system. As a way of starting, I am heating
> only
> > > the solvent, but the water box is not kept "cubic"
> >
> > You can use the "image" command in ptraj to map your atoms back to a unit
> > cell (no need to re-run the trajectory).
> >
>
> Dr Guillermina Estiu
> Chemistry Department
> Pennsylvania State University
> PA 16802 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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