If you use periodic boundaries, the box size needs to be more than twice the
cutoffs, to avoid calculation errors. I found this advice in the manual. (I
though reading it was a time waste, but more time I was going to waste doing
a wrong 1 ns simulation on a big system).
--------------------------------------------------
From: "Justin A. Lemkul" <jalem...@vt.edu>
Sent: Tuesday, March 03, 2009 12:00 PM
To: <rsoa...@fcfrp.usp.br>; "Discussion list for GROMACS users"
<gmx-users@gromacs.org>
Subject: Re: [gmx-users] simulation box
Quoting Ricardo Soares <rsoa...@fcfrp.usp.br>:
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).
In addition, you need to consider cutoff lengths and periodic boundary
conditions/minimum image convention. Some textbook reading is in order.
-Justin
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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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalem...@vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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