[gmx-users] Box size to be considered for a protein of length 500 residues and dimension of protein is 6.5nm maximum.
jalemkul at vt.edu
Fri May 18 22:08:27 CEST 2018
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
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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