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.
Mark
Cheers,
Shima
------------------------------------------------------------------------
*From:* Mark Abraham <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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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