[gmx-users] perfluorohexane pdb... again

Marcelo Silva jokler79 at hotmail.com
Tue Jan 11 17:50:51 CET 2011

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 

pdb link: http://www.filefactory.com/file/b4h4847/n/hexane.pdb

Thank you again and best regards

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