TURBOMOLE Users Forum

Forum General => Miscellaneous => Topic started by: idet2 on November 10, 2007, 12:04:02 PM

Title: Frozen coordinates
Post by: idet2 on November 10, 2007, 12:04:02 PM

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.

Title: Re: Frozen coordinates
Post by: christof.haettig on November 12, 2007, 08:28:16 AM

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

C.H.

Title: Re: Frozen coordinates
Post by: uwe on November 19, 2007, 03:04:38 PM

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 (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

  
  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 .

  
   
• 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     )

  
  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  )

  
  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
• 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

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

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=&

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

Title: Re: Frozen coordinates
Post by: idet2 on November 19, 2007, 05:17:24 PM

Thanks a lot UWE.

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

Regards,

G