[gmx-users] simulation box

[Ricardo Soares]

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).

Cheers,

Ricardo.


> 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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