AMBER Archive (2004)

Subject: Re: AMBER: Octahedron Box

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Jun 28 2004 - 10:43:21 CDT

you can center the trajectory on the protein
using ptraj.

----- Original Message -----
From: "Seonah Kim" <kim_at_qtp.ufl.edu>
To: <amber_at_scripps.edu>
Sent: Monday, June 28, 2004 11:30 AM
Subject: AMBER: Octahedron Box

> Dear All,
>
> I have a question about the explicit water model.
> I am using Trpcage with water model using Amber 8.
> When I run the VMD after MD, Trpcage is jumping around the water box.
Sometimes
> protein is in the middle of box but sometimes is at the edge of the box.
Can I
> put the protein inside of the box only?
>
> Thank you for your help in advance.
>
> Seonah Kim
>
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