[CPMD-list] Equilibration of organic molecules in water

[Axel Kohlmeyer]

>>> "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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--

=======================================================================
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.