[gmx-users] perfluorohexane pdb... again

[Marcelo Silva]

Angél,

I'm sending you my initial pdb in attachment. I chose the box size to 
fit the experimental density.
I am just trying to get simple properties of the pure compounds hexane 
and perfluorohexane and of a mixture 0.5 hexane/perfluorohexane (density 
mainly). But maybe I just need a long molecular dynamics equilibation 
step rather than simulated annealing to get a good starting configuration.
Perhaps what went "wrong" is that the system was at temperatures much 
higher than hexane boiling point and it started to form clusters.

Best regards,

Marcelo