[gmx-users] Box size to be considered for a protein of length 500 residues and dimension of protein is 6.5nm maximum.

[Justin Lemkul]

On 5/18/18 12:39 PM, SHYANTANI MAITI wrote:
> Dear all,
> What should be the value of d in editconf command for a protein-protein
> complex of 500residues and length of protein is 6.5nm maximum.
> I have simulated it using the command:
> editconf -f conf.gro -bt cubic -d 6 -o box.gro
> (considering 6 as the value of d).
> I have considered the value of as 6 such that the cubic box is of
> 12nm(d+d=6+6 from center of protein) length of each side, so that I can
> give space to the protein-protein complex for creating its trajectory. Is
> my concept correct?
> I have also tried with the value of d as 1. When I am checking the
> solvated.gro file for both d as 1and d as 6, I find that the protein is
> solvated properly in both cases.
> Can I consider the value of d as 1 instead of 6 for my specified
> protein-protein complex?

The solute-box buffer length depends on the force field (because of the 
required cutoffs) and has little to do with the protein itself. As long 
as you don't expect any large conformational changes or unfolding, then 
the typical approach is to set -d to the value of the longest cutoff 
required by your force field so you satisfy the minimum image 
convention. Then you have at least 2 cutoffs of buffer between images, 
which is a pretty safe approach to mitigate any potential water ordering 
effects if you try to shortcut things. This is not a hard and fast rule 
(and doubtless there will be people that would respond and argue about 
that approach), but it's a rule of thumb that you can apply and be 
pretty safe.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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