[gmx-users] Type of unit cell

Mark Abraham Mark.Abraham at anu.edu.au
Sat Apr 21 17:16:42 CEST 2012

On 22/04/2012 1:13 AM, Shima Arasteh wrote:
> So I can not change the type of unit cell in regenerating a job done 
> before, right?

You can't replicate the simulation (see, for example, 
http://www.gromacs.org/Documentation/Terminology/Reproducibility). You 
can attempt to replicate the observations. If you judge they're 
independent of box shape, then use whatever box you want.


> Cheers,
> Shima
> ------------------------------------------------------------------------
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Saturday, April 21, 2012 7:23 PM
> *Subject:* Re: [gmx-users] Type of unit cell
> On 22/04/2012 12:00 AM, Shima Arasteh wrote:
>> Dear Gomacs friends,
>> I'd like to know if it makes different in the last outcomes of a 
>> simulation when I change the box?
> Yes, it changes.
>> For example I use dodecahedron instead of cubic one. I just know that 
>> I need to add less numbers of water molecules.
> True. It's your call based on what you want to simulate.
> Mark
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