[CPMD-list] Equilibration of organic molecules in water

[Axel Kohlmeyer]

On Thu, 3 Mar 2005, Keta Jones wrote:

KJ> Dear Dr Axel,
KJ> 
KJ> I am very very sorry for the word cyclohexexanone. It
KJ> is actually cyclohexanone. My aim is to solvate either
KJ> benzene or cyclohexanone in water. If cyclohexanone
KJ> will be large enough what about benzene ?
KJ> 
KJ>  After going thhrough the following reference i.e 
KJ> J. Am. Chem. Soc.2004; 126(20); 6280-6286.
KJ>  Boero, M.; Ikeshoji, T.; Liew, C. C.; Terakura, K.;
KJ> Parrinello, M. I feel that this can be done. 

dear keta,

in your original mail, you did not mention, that
you would remove water molecules, so i had to assume
the worst case. of course the procedure proposed in
the paper you mentioned can be done. in my personal
opinon it would be simpler to set up a classical 
pre-equilibration, but this may be simply due to
the fact, that i have quite a bit of practice with that.
the classical equilibration will become problematic,
if you don't have a reasonable force-field parameters.
for benzene they _do_ exist. in fact there is a large
number of classical MD studies of benzene solutions
and benzene/water mixtures.
cyclohexanone can probably be done, too. remember that
for classical pre-equilibration you don't need perfect
force-field parameters, but only reasonable ones.

i don't know the details of the paper above, but 
i would want to do something similar, i'd freeze
the coordinates of all distant water molecules,
'dig' a large enough hole, add the new molecule,
and then optimize the coordinates for a limited
number of steps. in the following i would unfreeze
more and more and more coordinates and then do
either short MD runs or geometry optimizations,
depending on how much pointential energy you
have to remove. as mentioned in my previous mail,
you want to avoid sending a shockwave through
your system as it will ruin the dynamics.

regards,
	axel.

-- 
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Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
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If you make something idiot-proof, the universe creates a better idiot.