Thank you Angél and Stephane for your help
I also have another question. Using the pure hexane pdb (I am mixing
hexane and perfluorohexane), I've run simmulated annealing with a box of
500 molecules trying to obtain a good conformer distribution. The
heating steps were:
time (ps): 0 8 50 58 150
Temperature: 298 1000 298 1000 298
I don't if this is the best temperature program but I've converted the
trajectory to a pdb file (last time step) and using Avogadro I see a box
full of hexane molecules but the same conformer. Using Rasmol I see
different conformers and the box as several holes in it. What is wrong
here?
pdb link: http://www.filefactory.com/file/b4h4847/n/hexane.pdb
Thank you again and best regards
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