Hi,

I am trying to equilibrate an amorphous box with tryptophan molecules and I have few questions.

How do we calculate the density for an amorphous cell? I only have the crystal density.

When I use the cell calculation option from the amorphous cell some of the N-H bonds look bended or sometimes even the amide and benzene ring relative to each others. If I run an equilibration NPT on the box created things are not getting better.

Before I build the amorphous cell I have run a geometry optimisation using Forcite. The N atoms and C atoms in the rings after the calculations are aromatic type. I have use Compass forcefield for all the calculations. I have tried both Electrostatic Group base and Atom based and I get the same problem. I set the van der Waals at atom based. I have tried different density values and also ramping the density from a small value 0.6 to 1.3. Still didnt work.

If anyone can help me with this I will highly appreciate.

Thanks

Ioana