[gmx-users] box size

[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.
>

Hi,
did you use the "-d" option in editconf to create the box size?

> 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 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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