AMBER Archive (2009)

Subject: Re: [AMBER] part of the protein escaped from the water box

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Oct 15 2009 - 06:40:53 CDT

On Thu, Oct 15, 2009, qiaoyan wrote:
>
> I simulate a protein including 104 residues, the protein was
> surrounded by a periodic box of water molecules described by the
> TIP3P potential extended to a distance of 10.0A from any solute
> atom. After 6ns of constant-pressure simulation, part of the protein
> escaped from the waterbox,

This sounds like just an imaging problem. You can use the "image" command
in ptraj to re-center the protein in the unit cell. Remember that the program
only stores the coordinates of atoms in one unit cell, but all the surrounding
cells are really "there" in terms of the energy function.

...good luck....dac

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