AMBER Archive (2003)

Subject: Re: water box distortion

From: GUILLERMINA L ESTIU (gle10_at_psu.edu)
Date: Sat May 24 2003 - 10:34:11 CDT

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?

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