Thanks.
I read that it doesn't matter if the protein moves and even protrudes the box.
It's OK, but there is a question here; why doesn't the box move rather than the
protein?
Is it possible for box to be defined every step?, then the protein would stay
in the center of the box.
Sincerely,
Shima
________________________________
From: Mark Abraham <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Thursday, June 14, 2012 12:22 PM
Subject: Re: [gmx-users] protein near the edges of simulation box
On 14/06/2012 5:47 PM, Shima Arasteh wrote:
Dear gmx friends,
>
>
>I put a protein in a simulation box filled of water molecules and entered the
>mdrun command. After the simulation, I found the protein near one of the edges
>of the box and not in center. What is the problem? Anyone may suggest me?
>
>Does it mean that the simulation is meaningless?
>
>I expect the protein to stay in the center of box and goes unfold by passing
>the time.
>
>
See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
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