[gmx-users] gmx insert-molecules

[Li, Shi]

Dear GMX users,

I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to insert 10 molecule B into the system box. The problem is
molecule B is slightly larger than molecule A. So in some cases, I couldn't
insert the exact 10 molecules of B into the system. Is there a way to
automatically adjust the size of the box according to the radius of
molecule B, so that they can fit in? Or, is there a better solution to do
this?

Or, is there a way to ignore the overlapping of molecules? In that case,
even the inserted molecule is overlapping with surrounding molecules, it
can still be inserted in?

Many thanks,
Shi