[gmx-users] protein near the edges of simulation box

[Erik Marklund]

Hi,

All molecules diffuse. As such, proteins are expected to move about. Preventing them form doing so is essentially non physical, so you'd need a good and thought-through reason for doing so.

Erik

15 jun 2012 kl. 10.27 skrev Shima Arasteh:

> 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 <Mark.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
> 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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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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