[gmx-users] simulation box

Ricardo Soares rsoares at fcfrp.usp.br
Tue Mar 3 18:51:48 CET 2009

noob noob wrote:
> Dear all,
>  I am new about MD simulation and I have some questions about the box 
> size.
> I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 
> nm ) but now I change to a bigger molecules and increase the number of 
> molecules. So,the new system cannot fix into the previous box. 
> Therefore, I tried to Increase my box to a bigger one ( 20 nm x 20 nm 
> x 20 nm) which can fix the system nicely.
> So, is it compulsory to use certain box size in our system? or we just use
> any box size which our molecules can fix into it, then perform MD?
Sorry, I didn't see this other question of yours.
If you use a box that is much larger than the main molecule, you will 
need lots of water, which will be time-consuming. Otherwise, if you use 
a very small box, it may compromise the free movement of the protein.
So i say the best option is to scale the box size according to your 
specific molecule size. This is done within the editconf program. (see 
the gromacs manual for further reference).



> Sorry for the "stupid" questions.
> thanks for the comments.
> Alvin Chan.
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Ricardo Oliveira dos Santos Soares
Post-graduation Student in Biological Physics
University of Sao Paulo - USP
Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
Phone: 55 (16) 3602-4840
Curriculum Lattes - http://lattes.cnpq.br/0777038258459931

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