[CPMD-list] how to include water in QM part in a QMMM calculation

[Yong Zhang]

Dear Axel,

Thanks for your reply.


On 5/16/07, Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote:

>
>
> YZ> What is the difference between 999 and -999? When would those be used?
>
> please see
> http://www.cpmd.org/manual/node47.html
>
> and for more details have a look at detdof.F lines 230-250




> there are some oddities in your input, can you please explain
> how you did the setup your system. did you equilibrate it with
> gromos or amber? you gromos input looks as if you used amber,
> but then you have to set AMBER in the &QMMM section.


The system was setup initially using GROMOS. I generated the solute
(including NMA and 79 solute water molecules), then solvent was added
(solvent water).
The whole system was equilibrated in cpmd/gromos using "molecular dynamics
classical" with solute fixed. This is only a test run, so I suppose it is
ok.

The gromos input was modifed from the one in your example (from biocore), in
which case amber was used. What is difference between amber and gromos form
in this QM/MM calcualtion? How can I modify that to a gromos job?




> YZ> &QMMM
> YZ>   VERBOSE
> YZ>   GROMOS
> YZ>   WRITE LOCALTEMP
> YZ>   SPLIT
> YZ>   TOPOLOGY
>
> YZ> # NPM >= 0 number of (identical) solute molecules
> YZ> # NSM >= 0 number of (identical) solvent molecules
> YZ> #      NPM     NSM
> YZ>        1      429
> YZ> END
>
> also, if you want to make water molecules quantum, that are
> in the solvent section, you first have to convert them into
> solute molecules. for that you have to create a new topology
> and input file (either manually, or via the FLEXIBLE WATER
> keyword). see:
> http://www.cpmd.org/manual/node111.html


I added "flexible water" and the problem gone now. But I still do not
understand: what is the "solute water" for in gromos topology? or in other
word, under what situation should I use that?
One more question here, what was changed by "flexible water"? I checked the
two topology files, but did not realize any difference, like the bond
between two water H  atoms are still there.

Thanks

Yong
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