Hi,
define an internal coordinate and fix it. The procedure is described in the manual, but perhaps the tutorial is a little bit easier to read (there is a pdf file in the DOC directory of your Turbomole installation, or download it from our web site:
http://www.cosmologic.de/data/Turbomole_Tutorial_59.pdf. See chapter 7.4:
Constrained optimization)
A short How-To:
- run define
- Read in the coordinates by entering in the SPECIFICATION OF MOLECULAR GEOMETRY menu:
a coord - go to the INTERNAL COORDINATE MENU menu and choose
idef : SUB-MENU FOR INTERACTIVE DEFINITION OF INTERNAL COORDINATES
by entering idef you will get the following screen:
ENTER INTERNAL COORDINATE DEFINITION COMMAND
<x> <type> <indices>
WHERE <x> = k f d i
<type> = stre invr bend outp tors linc linp
comp ring pyrm bipy pris cube octa
THESE COMMANDS WILL BE EXPLAINED IN DETAIL IF YOU ENTER <x> <type> ? FOR
SOME CHOICE OF <x> AND <type> , E.G. k stre ?
DEFAULT=GO BACK TO INTERNAL MAIN MENU DISPLAY=dis
Hence, to define a fixed dihedral angle, use the f to set it to fixed type and tors for torsional angle.
Enter:
f tors ?
to get help and the detailed description about how to define the dihedral angle:
THE COMPLETE SYNTAX OF THIS COMMAND IS f tors <i> <j> <k> <l>
THE FIRST LETTER DEFINES THE STATUS OF THE INTERNAL COORDINATE
STATUS = f INDICATES AN INTERNAL COORDINATE WHICH WILL BE
KEPT AT A F(IXED) VALUE IN THE COURSE OF A GEOMETRY
OPTIMIZATION PROCEDURE.
THE COORDINATE TYPE tors IDENTIFIES A TORSIONAL ANGLE COORDINATE
THE TORSIONAL ANGLE <i>-<j>-<k>-<l> IS DEFINED WITH
RESPECT TO <j>-<k> AS BOND AXIS.
NOTE THAT TORSION COORDINATES DO N O T WORK IN
GEOMETRY OPTIMIZATIONS IF THE ANGLE <i>-<j>-<k> OR
THE ANGLE <j>-<k>-<l> GETS CLOSE TO 180 DEGREES !
IN THAT CASE YOU SHOULD RATHER USE THE COORDINATES linc
AND linp .
- Hint <Enter> until you reach the INTERNAL COORDINATE MENU again and check the first line:
INTERNAL COORDINATE MENU ( #ideg=174 #k=0 #f=1 #d=0 #i=0 )
the number of fixed internal coordinates is given: #f=1
Use disi to display the internal coordinates. - Hit <Enter> again to get back to the menu:
SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=60 SYMMETRY=c1 )
and there, use internal redundant coordinates to get the complete set of internal coordinates automatically, including the one that you have fixed:
ired
- If you want to be sure that your fixed internal coordinate has been used, call red_info, scroll back your window and check that the number of frozen coordinates is one:
red_info
$redundant
number_of_atoms 60
degrees_of_freedom 174
internal_coordinates 387
frozen_coordinates 1
- Now a usual geometry optimization with jobex will automatically be a constrained search.
Hint: ired will always check if fixed internal coordinates are already defined (definition is stored in the file
coord):
$intdef
# definitions of internal coordinates
1 f 1.0000000000000 stre 1 2 val= 2.74199
$redundant
number_of_atoms 60
degrees_of_freedom 174
internal_coordinates 387
frozen_coordinates 1
Values of frozen coordinates
2.74199000
# definitions of redundant internals
You can change the value of the internal coordinate. Here, it is the distance between atom 1 and 2. Just change the line:
$intdef
# definitions of internal coordinates
1 f 1.0000000000000 stre 1 2 val= 3.24199
and rerun
define.
define will read in cartesian AND internal coordinates and check if they are consistent:
CARTESIAN COORDINATES AND VALUES OF INTERNAL COORDINATES DO N O T AGREE !
ENTER COMMAND :
c : USE CARTESIAN COORDINATES TO ESTABLISH GEOMETRY (DEFAULT)
i : USE VALUES OF INTERNAL COORDINATES TO RE-SHAPE GEOMETRY
If you say
ihere, define will give you the possibility to enter the geometry menu:
DO YOU WANT TO CHANGE THE GEOMETRY DATA ? DEFAULT=n GOBACK=&
so say
y here.
Do
iredand continue as usual. Check your geometry after having finished the input with define: the structure is changed according to the new value of the internal coordinate.
Hope this helps,
Uwe
