[CPMD-list] Re: Equilibration of organic molecules in water

[Ian R. Greig]

Dear all,

Apologies for the partially formed message sent previously.

I was wondering whether anyone has any further comments on the various 
methods for equilibrating solute molecules in water.

The methods that seem to have been used are...

1) Perform a classical MD equilibration of the system prior to any CPMD 
simulation as suggested by Axel. This equilibration I assume is carried 
out in the NPT ensemble and the quantum box size used is the same as that 
from the classical equilibration.

2) Equilibrate a quantum system (presumably either derived as in 1 above
or by replacement of some number of water atoms but the solute of
interest) using Parrinello-Rahman dynamics (e.g. as per Gaigeot and Sprik
- J. Phys. Chem. B 107, 10344, 203) to obtain the appropriate box size.

Does anyone have comments on the relative suitability and computational 
expense of both methods? I imagine that method 2) (probably starting from 
an MM-derived system) is probably the most rigorous but that 1) will 
probably be alot quicker.

Additionally, it seems that any study of the reactivity of a small system
will probably be practically limited to Car-Parrinello dynamics. This will 
ignore any change in volume on reaction which might be quite significant?

Many thanks for your help and comments as always,

Ian

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                          Ian R. Greig

Chemistry Department                   
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irg20 at cantab.net
irg20 at chem.ubc.ca
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