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

[Axel Kohlmeyer]

On Wed, 16 May 2007, Yong Zhang wrote:

YZ> Dear Axel,

YZ> I do not have amber here, but I guess amber7togromos.x converts the amber
YZ> TOPOLOGY file into gromos topology, not the input file. (or maybe it does?).

amber7togromos.x takes the amber restart and topology and creates
a gromos compatible topology and input and coordinate file from it.

YZ> But what is the difference in the gromos input file for amber ff or gromos
YZ> ff?

the file format is the same, the parameters are different, and with 
the AMBER keyword in &QMMM a different functional form for bonds is
used, i.e. the quadratic one as in gromos87 and amber and not the
quartic one as in gromos96.

[...]

YZ> I realized that solvent atoms can not be treatted in QM section. In that
YZ> case, a error message was given clearly demonstrated that. So in this case,
YZ> I include some water molecules in the SOLUTE part. I did this by setting
YZ> NMOL=80 when builtup the topology using gromos:

you should take care that you _only_ put those water molecule into
solute that you intend to make QM, otherwise you will have two different
classical water types in your system.

if you want to put a different water into the QM region you
can just swap the coordinates in the gromos coordinate file
with the previous QM water. but you probably have to adjust
the coordinates so they are consistent with the rigid water
potential structure (depends on the tolerance of the shake
implementation).

[...]

YZ> By doing this way, when added one water into QM part, I did not get the
YZ> error message saying that "solvent can not be in QM". But, unfortunately, I
YZ> got another error related to the "shake" problem.

please make sure that your input and topology file and all 
related parameters are correct. it is impossible to verify
that without having all files at hand. the question with the
shake error is, _when_ does it happen? in the first step or
after the first step? is the gromos format output correct
after classical equilibration with CPMD.

YZ> Below I attached the two definition of water in gromos, one as solute and
YZ> one as solvent. And I used the solute one in my "solute"(the 79) and solvent
YZ> on in my "solvent" (429).
YZ> But I guess, as you indicated, I do not really need so many complex steps.
YZ> I can simply setup a real solute (NMA in my case) and added solvents to it,
YZ> then use "flexible water" to convert some solvent into solute and make
YZ> necessary changes in the crd file. Then it should work. I will try this.

yes. that is more straightforward in my experience.
also, in my experiments, i've almost completely avoided to
use gromos tools at all and was mostly editing the topology
and input files manually. for as long as you don't need to
reorder the solute part but merely append (small) molecules
it is rather straightforward.

[...]
YZ> > _use_ the cpmd/gromos qm/mm code regularly (i don't) would
YZ> > expand that part of the documentation and explain the motivation
YZ> > and proper protocols for setting up a QM/MM input. most of
YZ> > what i put in there quit a while ago is guessed from what
YZ> > the sourcecode does.
YZ> 
YZ> 
YZ> I really appreciate all your effort to make QM/MM accessible to more people.
YZ> I am sorry I did not help much so far since I am still hesitating at the
YZ> very initial steps. But anyway, hope this discussion is somewhat helpful for
YZ> others.

this was not addressed to you but to the many, many people reading
this, that actually do use the code a lot and should be much more 
competent than me.

cheers,
  axel.

YZ> 
YZ> Best wishes,
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
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.