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

[Axel Kohlmeyer]

>>> "IG" == Ian R Greig <irg20 at chem.ubc.ca> writes:

IG> Dear all,

dear ian,

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

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

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

yes. of course this can only work if you have adequate force field
parameters for the molecule in question. in my tests using SPC/E as 
water potential seemed to produce a water structure, that matches
the one of BLYP water quite closely.

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

what has been done, is to take a well equilibrated water restart,
determine the size of a hole needed for the molecule in question
and find the closest matching water cluster to be removed.
of course this works best for small molecules.

the most tricky setup to equilibrate with CPMD, that i have 
encountered so far, was a dense water layer inbetween a crystal slab. 

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

doing a parrinello-rahman run with CPMD is _very_ expensive. you need to
make sure, that the stress tensor is well converged with respect to
the plane wave cutoff, and that takes very much larger plane wave cutoff
than for a normal CP-MD. but also the run is then done with a constant 
number of plane waves, which means that the effective cutoff changes
with the size of the box. in short, you can do it, but you want to avoid
it unless you have no other way.

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

could you elaborate a little more on this. there are quite a few ways
to determine e.g. free energy surfaces, some of which are implemented in
cpmd. but of course any reaction that happens spontaneously and without
any additional driving in the timeframe available to CPMD simulations,
has to be very fast (e.g. proton transfers) and i cannot imagine how 
something like that would result in a large change in volume.

regards,
        axel.

IG> Many thanks for your help and comments as always,

IG> Ian

IG> ------------------------------------------------------------------
IG>                           Ian R. Greig

IG> Chemistry Department                   
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IG> Vancouver, British Columbia            
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IG> irg20 at cantab.net
IG> irg20 at chem.ubc.ca
IG> ------------------------------------------------------------------








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--

=======================================================================
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/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.