[gmx-users] perfluorohexane pdb... again

Ángel Piñeiro angel.pineiro at usc.es
Tue Jan 11 18:13:30 CET 2011

Hi Marcelo
1.- perfluorohexane is a quite rigid molecule so I wouldn't expect many
different conformations
2.- your simulation box is far away from the equilibrium
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.

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.



On Tue, 2011-01-11 at 16:50 +0000, Marcelo Silva wrote:

> 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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