Question

# Anybody familiar with the freezing of atoms in gaussian software?

If we use -1 for freeze the atoms all the direction of the atoms are freezes  but I want freeze atoms particularly one Cartesian axis just say Z-direction remaining two direction relaxes. Is it possible in Gaussian?

Ahmed Eid
Chemistry Department, Faculty of Science, Al-Azhar University, Egypt
I agree with Dr Vithaya's answer.
You can try also Z-matrix, there is an option in Gauss view to convert Cartesian coordinates to Z-matrix for this large number of atoms
1 Recommendation

Vithaya Ruangpornvisuti
Chulalongkorn University
Yes you can freeze atom(s) in molecule as partial optimization using Gaussian. It is very easy to set  gaussian input, as following condition.
(1) Input atoms must be in Cartesian coordinate,
(2) insert code number in between Atom name (i.e. O) and atomic x-value as,
(2.1) assignment code as number  = -1 if you want to freez  atom on that line,
(2.2) number = 0, if you want to let atom move in optimization process.
Pleas learn from following example:
%chk=example.chk
# hf/3-21g geom=connectivity
H2O vs C6H6
0 1
O 0 -2.09620750 1.02317579 1.79143348
H 0 -1.63026934 0.29352612 2.20629850
H 0 -2.41660654 1.62464460 2.46758415
H -1 -4.44172210 1.31649620 0.06952996
C -1 -3.34211810 1.31631320 0.06970996
C -1 -2.64473610 0.10833720 0.07039196
C -1 -2.64451710 2.52451920 0.06871396
C -1 -1.24957610 0.10833720 0.07039196
H -1 -3.19449510 -0.84397980 0.07084196
C -1 -1.24969210 2.52459720 0.06919296
H -1 -3.19463910 3.47680020 0.06776096
C -1 -0.55203810 1.31608820 0.07039196
H -1 -0.70006810 -0.84417580 0.07170696
H -1 -0.69949210 3.47674020 0.06913396
H -1 0.54764190 1.31616820 0.07102596
1 2 1.0 3 1.0
2
3
4 5 1.0
5 6 1.5 7 1.5
6 8 1.5 9 1.0
7 10 1.5 11 1.0
8 12 1.5 13 1.0
9
10 12 1.5 14 1.0
11
12 15 1.0
13
14
15
Goodluck,
VR
18 Recommendations

## Top contributors to discussions in this field

Do you want to freeze one particular variable?
2 Recommendations
If you need to freeze 1 particular variable, I would suggest
converting the structure into Z-Matrix format and then
freeze the variable(s) you want to be constant
1 Recommendation
Chammi Palehepitiya Gamage
University of Texas at Austin
You can freeze the whole atom I don't think you can do it for just a specific coordinate. I would ask them, they are pretty helpful. http://www.gaussian.com/g_tech/em_help.htm
Vithaya Ruangpornvisuti
Chulalongkorn University
Yes you can freeze atom(s) in molecule as partial optimization using Gaussian. It is very easy to set  gaussian input, as following condition.
(1) Input atoms must be in Cartesian coordinate,
(2) insert code number in between Atom name (i.e. O) and atomic x-value as,
(2.1) assignment code as number  = -1 if you want to freez  atom on that line,
(2.2) number = 0, if you want to let atom move in optimization process.
Pleas learn from following example:
%chk=example.chk
# hf/3-21g geom=connectivity
H2O vs C6H6
0 1
O 0 -2.09620750 1.02317579 1.79143348
H 0 -1.63026934 0.29352612 2.20629850
H 0 -2.41660654 1.62464460 2.46758415
H -1 -4.44172210 1.31649620 0.06952996
C -1 -3.34211810 1.31631320 0.06970996
C -1 -2.64473610 0.10833720 0.07039196
C -1 -2.64451710 2.52451920 0.06871396
C -1 -1.24957610 0.10833720 0.07039196
H -1 -3.19449510 -0.84397980 0.07084196
C -1 -1.24969210 2.52459720 0.06919296
H -1 -3.19463910 3.47680020 0.06776096
C -1 -0.55203810 1.31608820 0.07039196
H -1 -0.70006810 -0.84417580 0.07170696
H -1 -0.69949210 3.47674020 0.06913396
H -1 0.54764190 1.31616820 0.07102596
1 2 1.0 3 1.0
2
3
4 5 1.0
5 6 1.5 7 1.5
6 8 1.5 9 1.0
7 10 1.5 11 1.0
8 12 1.5 13 1.0
9
10 12 1.5 14 1.0
11
12 15 1.0
13
14
15
Goodluck,
VR
18 Recommendations
Matthew D. Miller
Semichem Inc.
I have performed calculations with a limited number of atoms frozen using cartesian coordinates (truncated protein with a ligand).  I suggest testing the file format shown by Dr. Ruangpornvisuti above.  The column flagged with 0 for atom optimization and -1 for atom freezing does work.  Upon completion of the calculation, files can opened and the frozen atoms will align correctly on top of each other.  This column is not required in an input file by default and is assumed to be 0 when not included.  This is described in the oniom section of the manual (search for freeze).
It is possible to use z-matrix coordinates to freeze atoms, although I am uncertain why this would be preferable to do.  If it is desirable to use z-matrix (use the readfreeze option), it is very important to list atoms that are frozen at the top because atoms which shift in position during optimization will be used as a reference point for the frozen atoms and the frozen atoms will not actually remain in the same position.  However, if the frozen atoms are listed first, each frozen atom will reference frozen atoms and it works.  The "notatoms" and list of atom numbers to be frozen should be included in the input file.  I had some challenges using the z-matrix and suggest using the cartesian coordinates.  Readfreeze is described in the following section:
I suggest you confirm the atom positions do not move by viewing the input and output files overlaid.
Good luck,
M
2 Recommendations
Indian Institute of Technology Kanpur
I don't know about the Z-matrix, but I had some 150 atoms to freeze, so I used the following trick.
1. Draw the atoms in Gaussview.
2. Go to edit > Atom Group, group the atoms so that there exists two groups where group 1 contains the atoms to freeze and group 2 to not to freeze (and vice versa).
3. Go to Group Actions > "Select atoms of Gaussian Group 1" to the top right corner.
4. To the top left corner, click Atom Group Class > Freeze.
Hope this helps.

2 Recommendations
Mallika Khare
Michigan Technological University
I can help with freezing of individual atoms in z-matrix:
Z-matrix: It includes the bond length, angle and dihedral angle of a particular atom in reference to other atom.
So, when you prepare your molecule in z-matrix format in Gaussian and open the file in notepad, it will show you something like this: I have taken example of NH3 molecule:
N1
H2 1 r2
H3 1 r3 2 a3
H4 1 r4 2 a4 3 d4
r2=1.0
r3=1.0
r4=1.0
a3=110.
a4=110.
d4=120.
This is a z-matrix of ammonia. Here r2, r3, r4, are the bond length, a3, a4 are the angles and d4 is a dihederal. Suppose I want to freeze atom N (numbered 1) and H atom (numbered 3) in this example. So, my z-matrix will look like this:
N1
H2 1 r2
H3 1 r3 2 a3
H4 1 r4 2 a4 3 d4
r2=1.0
r4=1.0
a4=110.
d4=120.
r3=1.0
a3=110.
Here you can see that to freeze H3 and N1 atoms I picked up the associated bond length and angle/dihederal and separated it from the main list. This is how we freeze atoms in z-matrix. While freezing there should always be ONE BLANK line between the main list of bonds & angles and the bonds & angles you want to freeze. Hope this helps. Good Luck!
4 Recommendations
Khulood Obaid
University of Kerbala
I agree with answer of Mr Vikaya
Ahmed Eid
Chemistry Department, Faculty of Science, Al-Azhar University, Egypt
I agree with Dr Vithaya's answer.
You can try also Z-matrix, there is an option in Gauss view to convert Cartesian coordinates to Z-matrix for this large number of atoms
1 Recommendation

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