AMBER Archive (2008)

Subject: AMBER: molecule drift out of water box?

From: Qiuting Hong (
Date: Fri Sep 19 2008 - 18:39:42 CDT

Dear Amber users,

I am doing MD for a mouse ubiquitin, 1wgg, which has a long side chain. When
I solvate the protein, I try solvateoct TIP3PBOX 12.0 and
solvateoct TIP3PBOX 10.0. And I find out that the size of solute vdw
bounding box is same: 36.162, 30.853, 52.074. So, I decide to use TIP3PBOX
10.0 since it has less water molecules.

In the amber tutorial, it asks us to reimage all the water molecules into
the original box. So I did it, and I find out that a very small part of my
protein side chain drift into the vacuum after 1ns.

However, if I don't reimage the water molecules into the original box, the
whole protein is still in water. I am wondering whether or not my protein
drifts out of water box. Do I trust the reimaged trajectory or the original

If my protein do drift out ot the water box, how do I fix it? I think I need
to enlarge the water box, but both TIP3PBOX 12.0 and TIP3PBOX 10.0 give me
the same size of water box. I know that if I don't truncate the waterbox, I
won't have this problem. But I don't want to use so many water molecule in
the simulation.

I am using amber 9.
Can somebody help me?

Thank you.

Qiuting Hong

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