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

[Axel Kohlmeyer]

On Wed, 16 May 2007, Yong Zhang wrote:


dear yong,

YZ> The system was setup initially using GROMOS. I generated the solute
YZ> (including NMA and 79 solute water molecules), then solvent was added
YZ> (solvent water).
YZ> The whole system was equilibrated in cpmd/gromos using "molecular dynamics
YZ> classical" with solute fixed. This is only a test run, so I suppose it is
YZ> ok.
YZ> 
YZ> The gromos input was modifed from the one in your example (from biocore), in
YZ> which case amber was used. What is difference between amber and gromos form
YZ> in this QM/MM calcualtion? How can I modify that to a gromos job?

the major difference is the force field. if you set up 
a job with gromos certain sections have 'predefined'
values in them. e.g.:
ATOMTYPENAME
BONDTYPE
BONDANGLETYPE
IMPDIHEDRALTYPE
DIHEDRALTYPE
LJPARAMETERS

if you prepare a job with amber the contents of
those are generated from the amber topology files
from amber7togromos.x

[...]

YZ> I added "flexible water" and the problem gone now. But I still do
YZ> not understand: what is the "solute water" for in gromos topology?
YZ> or in other word, under what situation should I use that?

sorry, i cannot follow what you did and i don't really
think that you've solved your problem (you only avoided the
symptom, which is worse IMO).

if you look at the gromos input file you have in the SYSTEM
section NPM and NSM. the first is the number of solute 'molecules'
(which can consist of more than one molecule) and the solvent.
the geometry of the solvent is determined by the sections 
SOLVENTATOM and SOLVENTCONSTR in the gromos topology.
the QM/MM implementation is done in a way, that those 
molecules/atoms _cannot_ be turned into QM atoms. if you
want them to become quantum, you have to rearrange the
coordinates in the .crd file, add/change the proper definitions
to the various sections in the gromos topology and input files.

the FLEXIBLE WATER flag can assist in that conversion, but
you have to check the resulting topology file carefully
and adjust the rest of the input.

YZ> One more question here, what was changed by "flexible water"? I checked the
YZ> two topology files, but did not realize any difference, like the bond
YZ> between two water H  atoms are still there.

this is impossible to tell without seeing/trying out 
all the inputs. the documentation in the manual gives
you some (minimal) hints, but the rest can only be
found out by reading the code.

it would be _very_ much appreciated when people who actually
_use_ the cpmd/gromos qm/mm code regularly (i don't) would 
expand that part of the documentation and explain the motivation
and proper protocols for setting up a QM/MM input. most of
what i put in there quit a while ago is guessed from what 
the sourcecode does.

cheers,
   axel.

YZ> 
YZ> Thanks
YZ> 
YZ> Yong
YZ> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.