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
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