[gmx-users] simulation box size

[Justin A. Lemkul]

Aditi Borkar wrote:
> Dear All,
> 
> While simulating a protein in a box of solvent, I know that the box
> size should be twice the length of the cut-off. So, if I am using a
> van der Waals cutoff of 1.4, does it mean that the box dimension
> should be atleast 2.8 nm from the periphery of the protein?
> 

Such a distance is not necessary.  If you have 2.8 nm to the box edge, then you 
have a 5.6-nm distance between periodic images, well in advance of what you 
need.  You really just have to ensure that your periodic images are separated by 
at least the cutoff.  Since box deformations can occur over the course this is 
typically not done; instead you might just use -d 1.4.

> Secondly, in the experimental conditions, my protein concentration is
> 1 mM. This accounts to 1 protein molecule occupying 1660 nm^3. For
> such a volume, I have to generate a box with -d = 3.7 in editconf. I
> feel that the box is too large and may compromise my computational
> time. Please comment
> 

Are you just simulating protein?  Then I would argue that the absolute 
concentration is unnecessary.  If you were simulating protein + ligand, then the 
ratio of the two might be important, but I don't often see simulations where 
they actually attempt to get the concentration right in explicit solvent 
(implicit is another story).

-Justin

> -Aditi Borkar,
> TIFR
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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