Forum General > Miscellaneous

Frozen coordinates

(1/1)

idet2:
Hello!

I want to use TM for a geometry optimization. In that I 'd like to have the dihedral angles of certain atoms frozen.
How can I do it?

I know that if I want to freeze an entire atom I just have to put an "f" next to it in the coord file that produced by the corresponding*.xyz using x2t. But I am not interesting in freezing the position of the entire atom.
So using the *.xyz file is something that doesn't help.

If I save the geometry file as a "Gaussian/Gamess" type then I have the distances, angles and dihedrals separated.  But how can I insert that geometry to TM and more how can I specify what I want to be frozen?

If someone can post an example of an input geometry file that would be great.

Regards,

G.

christof.haettig:
It's explained in the manual in the section "internal coordinate menu" and
it's subsections...

C.H.

uwe:
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:

 
--- Quote ---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
--- End quote ---

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:


--- Quote ---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 .
--- End quote ---

 
* Hint <Enter> until you reach the INTERNAL COORDINATE MENU again and check the first line:


--- Quote --- INTERNAL COORDINATE MENU  ( #ideg=174     #k=0    #f=1    #d=0    #i=0     )
--- End quote ---

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:


--- Quote --- SPECIFICATION OF MOLECULAR GEOMETRY ( #ATOMS=60    SYMMETRY=c1  )
--- End quote ---

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:


--- Quote ---red_info

$redundant
     number_of_atoms            60
     degrees_of_freedom        174
     internal_coordinates      387
     frozen_coordinates          1
--- End quote ---

* 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):


--- Quote ---$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
--- End quote ---

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:


--- Quote --- 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
--- End quote ---

If you say

i

here, define will give you the possibility to enter the geometry menu:


--- Quote --- DO YOU WANT TO CHANGE THE GEOMETRY DATA ?  DEFAULT=n  GOBACK=&
--- End quote ---

so say y here.

Do

ired

and 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

idet2:
Thanks a lot UWE.

I 'll try it and hopefully I 'll manage to get it work.

Regards,

G

Navigation

[0] Message Index