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Hi Marcelo<BR>
1.- perfluorohexane is a quite rigid molecule so I wouldn't expect many different conformations<BR>
2.- your simulation box is far away from the equilibrium<BR>
3.- you should inform about which force field and simulation conditions are you using, for instance: was your simulation run at constant volume or constant pressure? it is better if you provide your mdp file and specify your force field.<BR>
<BR>
Since more than half of your simulation box is empty and the PFH molecules are aggregates like in cubes it seems clear that you are ages away from the equilibrium.<BR>
<BR>
Cheers,<BR>
<BR>
Ángel.<BR>
<BR>
<BR>
<BR>
<BR>
On Tue, 2011-01-11 at 16:50 +0000, Marcelo Silva wrote:
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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: <A HREF="http://www.filefactory.com/file/b4h4847/n/hexane.pdb">http://www.filefactory.com/file/b4h4847/n/hexane.pdb</A>
Thank you again and best regards
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