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Igor Polyakov
polyakoviv@gmail.com

If u set nzvar=3n-6 you will need to provide correct $zmat group with 3n-6 internal coordinates.

Best wishes, Igor



On Wed Jul 15 '09 4:27am, Thomas Patko wrote
--------------------------------------------
>Hello Igor:

>Once again thank you for the tips.  Looking at my output files the search was indeed run in Cartesian coordinates (explains why it ran a bit slow).  The full part of this portion of the output file was:

>-----------------------------
>          STATIONARY POINT LOCATION RUN
>          -----------------------------

> OBTAINING INITIAL HESSIAN, HESS=GUESS  
> DIAGONAL GUESS HESSIAN IN CARTESIAN COORDS IS H(I,I)=  0.3333

>          PARAMETERS CONTROLLING GEOMETRY SEARCH ARE
>          METHOD =GDIIS               UPHESS =BFGS    
>          NNEG   =         0          NFRZ   =         0
>          NSTEP  =       256          IFOLOW =         1
>          HESS   =GUESS               RESTAR =         F
>          IHREP  =         0          HSSEND =         F
>          NPRT   =         0          NPUN   =         0
>          OPTTOL = 1.000E-04          RMIN   = 1.500E-03
>          RMAX   = 1.000E-01          RLIM   = 7.000E-02
>          DXMAX  = 3.000E-01          PURIFY =         F
>          MOVIE  =         F          TRUPD  =         T
>          TRMAX  = 5.000E-01          TRMIN  = 5.000E-02
>          ITBMAT =        10          STPT   =         F
>          STSTEP = 1.000E-02          PROJCT=          T
>          MAXDII =        20          NSKIP  =         2
>1NSERCH=   0

>It sounds like if I simply set NZVAR=3N-6 for my system and do not provide any $ZMAT input at all, then the geometry optimization search should be conducted in internal coordinates (but NOT with DLC) using the MOPAC style Z-Matrix that I specify in $DATA to construct the international coordinates?

>NZVAR = 0 Use Cartesian coordinates (default).
>= M If COORD=ZMT or ZMTMPC and a $ZMAT is not given:
>the internal coordinates will be those defining
>the molecule in $DATA. In this case, $DATA must
>not contain any dummy atoms. M is usually 3N-6,
>or 3N-5 for linear.

>Do I have it correct and is such an approach a good idea or must I specify give $ZMAT?  There is nothing special about this system that I would think necessitates me providing $ZMAT.

>I should mention that although slow the structures from the Cartesian optimization result was good, and I would like the international coordinate geometry optimization to yield something quite similar.

>Thank you again for all of the suggestions and assistance.

>Cheers,

>Thomas

>On Tue Jul 14 '09 11:17pm, Igor Polyakov wrote
>----------------------------------------------
>>Hi again,

>>I'm pretty sure that when u put nzvar=0 the optimization runs in cartesian coordinates. the file exam01 in standard PC GAMESS distribution states:

>>! EXAM01.
>>!    1-A-1 CH2    RHF geometry optimization using GAMESS.
>>!
>>!    Although internal coordinates are used (COORD=ZMAT),
>>!    the optimization is done in Cartesian space (NZVAR=0).

>>So if u want to turn off the dlc and use internal ccordinates for optimization u should provide correct nzvar value along with correct $zmat group.

>>Best luck, Igor.

>>P.S.: the reason i wanted to see the input file is actually this line:

>>          -----------------------------
>>          STATIONARY POINT LOCATION RUN
>>          -----------------------------

>> OBTAINING INITIAL HESSIAN, HESS=GUESS  
>> DIAGONAL GUESS HESSIAN IN CARTESIAN COORDS IS

>>when u do activate internal coordinates the output is

>>          -----------------------------
>>          STATIONARY POINT LOCATION RUN
>>          -----------------------------

>> OBTAINING INITIAL HESSIAN, HESS=GUESS  
>> DIAGONAL GUESS HESSIAN IN INTERNAL COORDS IS
>>
>>
>>On Tue Jul 14 '09 9:40pm, Thomas Patko wrote
>>--------------------------------------------
>>>Hello Igor:

>>>Thank you for the reply.  The research group that I am collaborating with would rather not release output files for this particular project on public forums.  Is is possible to answer my question without the output file based upon the general syntax of the options for this RHF job?

>>>What part of the output file would have the answer to my question?  Any keyword that contains the answer would allow me to readily search for the appropriate portion of the output.

>>>Thanks,

>>>Thomas

>>>On Tue Jul 14 '09 6:45pm, Igor Polyakov wrote
>>>---------------------------------------------
>>>>Hello,

>>>>Actually in the PC GAMESS output file u can find the answer to your question. We could discuss it further given the output file.

>>>>best regards, Igor

>>>>On Tue Jul 14 '09 4:52pm, Thomas Patko wrote
>>>>--------------------------------------------
>>>>>Dear Firefly Users:

>>>>>I am performing RHF optimizations for various conformations of some biological systems that I wish to model with force field methods.  In order to obtain the necessary charges with R.E.D. (http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/http://q4md-forcefieldtools.org/RED/) I need to get good geometry optimization that result in biological relevant conformations.  When I used the DLC optimization engine, I got the lowest energy conformation, but as it turned out not a biologically relevant one (see options below).

>>>>> $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE
>>>>>       ICHARG=0 MULT=1 COORD=ZMTMPC nzvar=348 maxit=100
>>>>> $END
>>>>> $system mwords=100 timlim=1000000 kdiag=0 nojac=1 $end
>>>>> $p2p p2p=1 dlb=1 $end
>>>>> $scf dirscf=.t. $end
>>>>> $statpt nstep=1024 method=gdiis flags=0 noreg=10 regtol=1.5 $end
>>>>> $zmat dlc=1 auto=1 $end
>>>>> $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 $END

>>>>>When I simply removed the nzvar option (this should set it to the default of zero) then the optimizations yielded optimized structures that were biologically relevant conformations.

>>>>>My question is what optimization engine is then actually used then nzvar is zero?

>>>>>I suspect that the $zmat dlc=1 auto=1 $end is then completely ignored (and thus could be removed on the options), correct?  Are any other options also then ignored?  Is this search still conducted in internal coordinates (initial structure is provided as MOPAC style z-matrix) but just not using the DLC engine?  Should this still be faster than conducting such a search in Cartesian coordinates, correct?

>>>>>Regards,

>>>>>Thomas