[gmx-users] Regarding setting up the simulation box

[vijayakumar gosu]

Dear all,

i am performing molecular dynamics for large complex with ~500,000 atoms. I
have considered cubic box with 1nm distance from the molecule to the wall
of the box. however this takes huge number of water molecules, hence i have
manually visualized and edited the box inorder to reduce the water
molecules. The complex is stable throughout dynamics for 25ns. however i am
bit skeptic whether this approach is correct, because not sure the molecule
is exactly at the center of the box and also i have not checked the
distance between the molecule and the wall of the box before md run. could
you please comment on it?

Thanks