[CPMD-list] Equilibration of organic molecules in water

[Keta Jones]

Dear Dr Axel,

I am very very sorry for the word cyclohexexanone. It
is actually cyclohexanone. My aim is to solvate either
benzene or cyclohexanone in water. If cyclohexanone
will be large enough what about benzene ?

 After going thhrough the following reference i.e 
J. Am. Chem. Soc.2004; 126(20); 6280-6286.
 Boero, M.; Ikeshoji, T.; Liew, C. C.; Terakura, K.;
Parrinello, M. I feel that this can be done. 

In this article they cleaved the required space,
corresponding to four water monomers, to allocate the
cyclohexanone oxime and reequili-brated for about 5
ps.
Here the pre equilibrated co-ordinates of 64 water
molecules have taken for the cyclohexanone study.

So I want to know how this can be done, means some
hints.

For I was confused regarding that DUMP files in moldy
input file. I will see it again.

Many many thanks to Dr Axel for this superb job.

regards,
keta




--- Axel Kohlmeyer
<axel.kohlmeyer at theochem.ruhr-uni-bochum.de> wrote:

> 
> >>> "KJ" == Keta Jones <ketajone at yahoo.com> writes:
> 
> KJ> Dear All,
>                                                     
>  
> dear keta,                                          
>            
>                                 
> KJ> I have a pre-equilibrated structure of 107 water
> KJ> molecules and one cl- ion. Now I want to study
> KJ> one organic molecule( cycloxexanone ) in 107
> water.
> KJ> I somehow feel that cl- can be replaced by
> KJ> cyclohexanone. It will be great if someone can
> guide
> KJ> me to do this in details.
>           
> sorry to disagree, but the cyclohexanone (i assume
> you
> mean that, since i am not aware of a compound named 
> cycloxexanone) molecule is too large. if you would
> find 
> a way to squeeze it in there, you would get a
> _massive_ 
> soundwave running through your system (and it won't
> stop
> at the borders due to the PBC).
>                                 
> KJ> Are there any easy other fast(in terms of
> eulibration
> KJ> period) programmes so that I can
> KJ> equlibrate these systems there and after that I
> can
> KJ> study in CPMD ? From Aexl's webpage I came
> across
> 
> for a molecule like this solvated in water most
> classical MD 
> codes would do. you simply need a reasonable set of
> force 
> field parameters.
> 
> KJ> moldy.But can it handle the molecule like
> KJ> cyclohexanone in water ? or will it be easy to
> extract
> KJ> the input for CPMD for such system from moldy. I
> had
> KJ> problems getting xyz format from moldy.
> 
> why? running mdshak -c -f xyz on a moldy text mode
> restart 
> used to work nicely for me. ;-)
> 
> moldy only works for rigid molecules, and defining
> the parameters
> for a larger molecule can be tedious. you may want
> to have
> a look at the gromacs code instead
> (http://www.gromacs.org/).
> if you are lucky, you can find a contributed
> topology file
> for your molecule (they have a sizable collection).
> you only have to be careful with the coordinates.
> .gro files
> are in nanometers, so you have to multiply
> accordingly or
> convert them to .pdb or .xyz.
>                                                     
>  
> regards,
>         axel.
>                                 
> KJ> Please help.Help will be greatly appreciated.
>                                                     
>  
>                                                     
>  
>                                 
> KJ> Thanks in advance
> 
> 
> KJ> =====
> KJ> Keta
> KJ>
>
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> 
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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.
> 


=====
Keta
**************************************************************************************


	
		
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