[gmx-users] Solvating in a solvent other than water

[Pallavi Banerjee]

Hello Users,

I have a system of three polymer chains (30 monomers), all of which I
insert into a polymer matrix (5 monomers). I have an equilibrated box of
the matrix that would act as the solvent in my case. Since this non-aqueous
solvent box is too small, I expand it using genconf. But, on energy
minimizing this box, it forms blocks within the box, which precludes me
from equilibrating it. How do you circumvent this?

Thanks in advance.

-Pallavi Banerjee