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

SHYANTANI MAITI shyantani.maiti at gmail.com
Fri May 18 18:40:02 CEST 2018

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?
Thank you,

Best regards,
*Shyantani Maiti*

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