AMBER Archive (2009)

Subject: Re: [AMBER] protein protrudes from unit cell

From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Wed Mar 18 2009 - 04:08:41 CDT

On Wed, 2009-03-18 at 16:59 +0800, Jeffrey wrote:
> Dear amber users,
>
> After about 5ns NPT simulation, the protein protruded from the unit cell.
> the ligand in one protein of the dimmer run away from the binding pocket
> ntb = 2

You need to understand periodic boundary conditions. Have a look at the
iwrap option.

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