7.1. Flexibility

In this section, we will describe how to set molecular flexibility for geom.

7.1.1. topgen

There is a small tool called topgen in ABCluster that can be used to generate bonding very conveniently. Assume you have an organic molecule aip.xyz that is in standard XYZ format:

aip.xyz

113
AIP(+1)
N  10.45900000  -12.94900000   -8.94000000
H  10.14300000  -12.08200000   -9.34300000
H  11.09900000  -12.80100000   -8.17700000
H   9.66400000  -13.46100000   -8.55100000
C  11.12800000  -13.81000000   -9.92500000
H  10.48100000  -13.86000000  -10.80200000
C  11.21100000  -15.19900000   -9.28200000
O  11.48200000  -15.27400000   -8.08600000
C  12.52800000  -13.25600000  -10.32800000
H  13.18900000  -13.32500000   -9.46100000
C  12.50400000  -11.77400000  -10.78600000
H  11.61400000  -11.56800000  -11.38000000
H  13.33800000  -11.59800000  -11.46700000
C  13.18200000  -14.11500000  -11.43200000
H  14.17300000  -13.74000000  -11.68900000
H  12.58500000  -14.11600000  -12.34500000
H  13.32000000  -15.15200000  -11.12300000
N  10.86100000  -16.25800000  -10.02800000
H  10.63200000  -16.06600000  -10.99200000
C  12.65700000  -10.74000000   -9.65700000
H  12.73000000   -9.73500000  -10.07300000
H  13.57000000  -10.91400000   -9.08500000
H  11.82400000  -10.73000000   -8.95800000
C  10.63500000  -17.66700000   -9.63800000
H  10.42500000  -18.14800000  -10.59400000
C   9.32200000  -17.82400000   -8.85000000
O   8.44600000  -18.59600000   -9.23100000
C  11.85000000  -18.46100000   -9.07300000
H  12.67900000  -18.38800000   -9.77700000
H  11.58400000  -19.51900000   -9.05700000
C  12.34800000  -18.12800000   -7.66200000
O  11.63600000  -18.31400000   -6.68200000
N   9.15900000  -16.99400000   -7.82000000
H   9.97600000  -16.44000000   -7.57700000
N  13.57300000  -17.63100000   -7.53200000
H  14.15700000  -17.47000000   -8.33800000
H  13.90400000  -17.39300000   -6.61000000
C   7.91700000  -16.59300000   -7.18800000
H   7.17100000  -16.53900000   -7.98100000
C   8.12600000  -15.13200000   -6.75300000
O   8.58800000  -14.32500000   -7.56700000
C   7.45500000  -17.63700000   -6.13700000
H   8.13900000  -17.64100000   -5.28900000
H   7.47900000  -18.64500000   -6.55300000
S   5.76100000  -17.29100000   -5.53200000
N   7.75900000  -14.75500000   -5.52100000
H   7.33100000  -15.46600000   -4.94500000
C   7.84900000  -13.41900000   -4.90300000
H   7.63700000  -13.58400000   -3.84500000
C   4.79400000  -17.78100000   -6.98300000
O   5.31900000  -18.26600000   -7.98300000
C   6.75400000  -12.45200000   -5.39100000
O   6.36800000  -11.52400000   -4.68400000
C   9.26200000  -12.81100000   -4.98000000
H   9.52900000  -12.52000000   -5.99400000
H  10.01500000  -13.51100000   -4.61600000
H   9.32600000  -11.91300000   -4.36400000
N   6.23100000  -12.71300000   -6.58600000
H   6.63300000  -13.48600000   -7.10100000
C   5.06800000  -12.13300000   -7.22300000
H   4.39300000  -11.78600000   -6.43700000
C   4.34200000  -13.27600000   -7.94400000
O   4.98800000  -14.22300000   -8.40500000
C   5.45000000  -10.90600000   -8.08100000
H   5.68700000  -10.08200000   -7.40700000
H   4.57100000  -10.57200000   -8.63400000
C   6.59600000  -11.05600000   -9.08100000
N   3.00400000  -13.22600000   -7.97800000
H   2.56500000  -12.44000000   -7.52100000
C   6.46800000  -11.89100000  -10.21300000
H   5.57000000  -12.47000000  -10.37200000
C   7.77500000  -10.29500000   -8.91600000
H   7.88200000   -9.63800000   -8.06300000
C   2.08200000  -14.21600000   -8.54300000
H   1.10200000  -13.74300000   -8.47200000
C   7.49800000  -11.95200000  -11.17200000
H   7.38000000  -12.57800000  -12.04600000
C   8.79400000  -10.33800000   -9.88700000
H   9.66700000   -9.70800000   -9.77900000
C   2.02900000  -15.45100000   -7.63000000
O   1.11000000  -15.59700000   -6.82700000
C   2.36100000  -14.49400000  -10.05000000
H   3.31200000  -15.01000000  -10.17600000
H   2.50200000  -13.52900000  -10.53900000
C   8.65300000  -11.16400000  -11.01900000
H   9.41100000  -11.17300000  -11.78900000
C   1.27900000  -15.25700000  -10.85600000
H   1.58500000  -15.16900000  -11.90000000
N   3.04600000  -16.31000000   -7.73200000
H   3.78900000  -16.04200000   -8.36900000
C   1.22600000  -16.76700000  -10.57000000
H   0.61600000  -17.28000000  -11.31500000
H   0.78900000  -16.98800000   -9.59700000
H   2.22000000  -17.21500000  -10.60300000
C  -0.11500000  -14.61600000  -10.76300000
H  -0.55300000  -14.73700000   -9.77100000
H  -0.80200000  -15.07400000  -11.47600000
H  -0.07800000  -13.55000000  -10.98700000
C   3.29500000  -17.48200000   -6.90300000
H   3.05400000  -17.20100000   -5.87700000
C   2.37100000  -18.65600000   -7.32500000
H   2.62500000  -18.97100000   -8.33900000
H   1.35100000  -18.27900000   -7.39600000
C   2.32400000  -19.89900000   -6.40000000
H   1.49800000  -20.50500000   -6.77600000
C   3.56800000  -20.80000000   -6.48700000
H   3.83500000  -21.01000000   -7.52400000
H   3.38400000  -21.75900000   -6.00000000
H   4.43500000  -20.35800000   -5.99900000
C   1.97700000  -19.55500000   -4.94300000
H   1.08500000  -18.93000000   -4.88600000
H   2.79000000  -19.02600000   -4.44400000
H   1.77800000  -20.45900000   -4.36600000

This molecule has a lot of rotatable bonds and some rings. In principle, you can manually provide these flexibility information for geom, but you can use to topgen instead:

$ topgen aip.xyz

There are 3 files related to this work:

• aip.gjf: The molecule in GJF format containing bonding information for reference.

• aip-bonding.xyz: The molecule in XYZ format containing bonding information. You can find the following after coordinates:

aip-bonding.xyz

H   2.79000000  -19.02600000   -4.44400000
H   1.77800000  -20.45900000   -4.36600000

1 2 1.0 3 1.0 4 1.0 5 1.0
2
3
4
5 6 1.0 7 1.0 9 1.0
6
7 8 2.0 18 1.0
8
9 10 1.0 11 1.0 14 1.0
10
.. omitted ..
110 111 1.0 112 1.0 113 1.0
111
112
113

This bonding information is completely compatible with GaussView. Since there are 113 atoms, there will be 113 lines of bonding information for every atom. 1 2 1.0 3 1.0 4 1.0 5 1.0 means that atom 1 forms a bond with order 1.0 with atom 2, 3, 4, and 5. Note that only the bonding atoms with indices larger than this atom are written. For example, 5 6 1.0 7 1.0 9 1.0 `` indicates that atom ``5 bonds with atom 6, 7, and 9. Its bonding with atom 1 is not written here but in the line 1 2 1.0 3 1.0 4 1.0 5 1.0. Only the bonds with order 1.0 are treated as flexible bonds. The ones with order 2.0, 3.0, etc are treated as non-rotatable.

You must provide an XYZ file with bonding information to geom if you want ABCluster to explicitly consider flexibility.

• aip-cycles.txt: It lists cycles in this molecule.

aip-cycles.txt

38 40 46 48 52 58 60 62 68 74 80 89 99 50 45 42
67 70 76 85 78 72

This means that there are two rings in this molecule: a 16-membered ring composed of atom 38, 40, …, 45, and 42 and a 6-membered ring composed of atom 67, …, 72.

These lines can be directly used in the input of geom.

Tip

Note that topgen does not detect if a ring is rigid or not. For the above example, ring 67 70 76 85 78 72 is a benzene so it should not be deformed during conformation search.

7.1.2. Set up Flexibility in Input Files

You need to set flexibility in component block of an input file:

geom.inp

components
  aip-bonding.xyz 1
  fix 0 0 0 0 0 0
  ****
  water.xyz 100
  random -5 -5 -5 5 5 5
  ****
end

As described in Control the Cluster Shape, this means that we fix molecule AIP at position (0, 0, 0) without rotation, and randomly put 100 water in the box defined by (-5, -5, -5) and (5, 5, 5). Note that now AIP is still rigid since you do not assign flexibility.

You can set flexibility between the placement way and ****:

geom.inp

components
  aip-bonding.xyz 1
  fix 0 0 0 0 0 0
  nH nH
  38 40 46 48 52 58 60 62 68 74 80 89 99 50 45 42
  ****
  water.xyz 100
  random -5 -5 -5 5 5 5
  ****
end

Here nH nH and 38 40 46 48 52 58 60 62 68 74 80 89 99 50 45 42 are the flexible degrees of freedom to be sampled. There can be arbitrary lines of flexibility:

• 5 or more atomic indices: defines a flexible ring. This ring will be deformed during global optimization by geom. Say, 38 40 46 48 52 58 60 62 68 74 80 89 99 50 45 42 is a ring defined by atom 38, …, 42.

• 2 characters: defines flexible bonds. These bonds will be rotated during global optimization by geom. Note that there are two useful wildcards: * (any atom) and nH (any non-hydrogen atom). Now bonds can be defined in many forms:

  • 23 49 The bond between atom 23 and 49.

  • C C All bonds between C and C.

  • C N All bonds between C and N.

  • nH nH All bonds between non-hydrogen atoms.

  • * * All bonds.

  • 15 * All bonds between atom 15 and any atoms.

  • 15 nH All bonds between atom 15 and any non-hydrogen atoms.

7.1.3. Some Examples

geom.inp

components
  aip-bonding.xyz 1
  fix 0 0 0 0 0 0
  nH nH
  ****
end

All bonds between non-hydrogen atoms are rotatable.

geom.inp

components
  aip-bonding.xyz 1
  fix 0 0 0 0 0 0
  18 19
  45 50
  64 nH
  67 70 76 85 78 72
  ****
end

Bonds between 18 and 19, 45 and 50, 64 and any non-hydrogen atoms, are rotatable. The ring 67 70 76 85 78 72 is deformable.

geom.inp

components
  aip-bonding.xyz 1
  fix 0 0 0 0 0 0
  C C
  ****
end

All bonds between C and C are rotatable.

geom.inp

components
  aip-bonding.xyz 1
  fix 0 0 0 0 0 0
  nH nH
  38 40 46 48 52 58 60 62 68 74 80 89 99 50 45 42
  67 70 76 85 78 72
  ****
end

All bonds between non-hydrogen atoms are rotatable. The ring 67 70 76 85 78 72 and 38 40 46 48 52 58 60 62 68 74 80 89 99 50 45 42 are deformable.

Now you can use geom to do conformation search and global optimization of clusters of highly flexible units!

Tip

As mentioned above, ring 67 70 76 85 78 72 is a benzene so it should NOT be deformed during conformation search. But if you write here, it will be forcefully deformed, although during optimization it may probably go back to a plane.