ClayFF data file

[martinhp27]

Dear all
I'm currently trying to implement ClayFF into MDMC and I think the best way to do so, is to create a data file similar to OPSLAA.
I found the following data file in lammps github (https://github.com/lammps/lammps/tree/master/tools/msi2lmp/frc_files)

If you have some good ideas how to understand this frc file or change it to the dat file format, please let me know :)

• Martin

!CLAYFF forcefield

#atom_types cvff

!Ver Ref Type Mass Element Connections Description and charge
!---- --- ---- ---------- ------- -----------------------------------------
1.0 1 st 28.08550 Si 4 tetrahedral silicon 2.1
1.0 1 ao 26.98154 Al 6 octahedral aluminum 1.575
1.0 1 at 26.98154 Al 4 tetrahedral aluminum 1.575
1.0 1 mgo 24.30500 Mg 6 octahedral magnesium 1.36
1.0 1 mgh 24.30500 Mg 6 hydroxide magnesium 1.05
1.0 1 cao 40.08000 Ca 6 octahedral calcium 1.36
1.0 1 cah 40.08000 Ca 6 hydroxide calcium 1.05
1.0 1 feo 55.84700 Fe 6 octahedral iron 1.575
1.0 1 lio 6.941000 Li 6 octahedral lithium 0.525
1.0 1 ob 15.99940 O 2 bridging oxygen -1.05
1.0 1 obss 15.99940 O 3 oxygen double sub. -1.2996
1.0 1 obts 15.99940 O 2 oxygen tet. sub. -1.1688
1.0 1 obos 15.99940 O 2 oxygen oct. sub. -1.1808
1.0 1 ohs 15.99940 O 2 hydroxyl O sub. -1.0808
1.0 1 oh 15.99940 O 2 hydroxyl O -0.95
1.0 1 oh- 15.99940 O 1 hydroxide O
1.0 1 o* 15.99940 O 2 spc water O -0.82
1.0 1 ho 1.007970 H 1 hydroxyl H 0.425
1.0 1 h* 1.007970 H 1 spc water H 0.41
1.0 1 Na 22.99000 Na 0 sodium ion 1.0
1.0 1 K 39.10 K 0 potassium ion 1.0
1.0 1 Cs 132.9100 Cs 0 cesium ion 1.0
1.0 1 Ca 40.07980 Ca 0 calcium ion 2.0
1.0 1 Ba 137.3300 Ba 0 barium ion 2.0
1.0 1 Mg 24.3050 Mg 0 magnesium ion 2.0
1.0 1 Sr 87.6200 Sr 0 strontium ion 2.0
1.0 1 Pb 207.2000 Pb 0 lead ion 2.0
1.0 1 Cl 35.45300 Cl 0 chloride ion -1.0

#equivalence cvff

Equivalence table for any variant of cvff

! Equivalences
! -----------------------------------------
!Ver Ref Type NonB Bond Angle Torsion OOP
!---- --- ---- ---- ---- ----- ------- ----
1.0 1 h h h h h h

#auto_equivalence cvff_auto

! Equivalences
! -----------------------------------------
!Ver Ref Type NonB Bond Bond Angle Angle Torsion Torsion OOP OOP
! Inct End atom Apex atom End Atoms Center Atoms End Atom Center Atom
!---- --- ---- ---- ------ ---- ---------- --------- --------- ----------- -------- -----------
2.0 18 h h h h_ h_ h_ h_ h_ h_ h_

#hbond_definition cvff

#morse_bond cvff

E = D * (1 - exp(-ALPHA*(R - R0)))^2

!Ver Ref I J R0 D ALPHA
!---- --- ---- ---- ------- -------- -------
2.3 23 no o- 1.2178 140.2486 2.0000

#quadratic_bond cvff

E = K2 * (R - R0)^2

!Ver Ref I J R0 K2
!---- --- ---- ---- ------- --------
2.1 28 o* h* 1.0000 553.9350
2.1 28 oh ho 1.0000 553.9350
2.1 28 ohs ho 1.0000 553.9350

#quadratic_angle cvff

E = K2 * (Theta - Theta0)^2

!Ver Ref I J K Theta0 K2
!---- --- ---- ---- ---- -------- -------
1.0 1 h* o* h* 109.4700 45.7530

#torsion_1 cvff_auto

E = Kphi * [ 1 + cos(n*Phi - Phi0) ]

!Ver Ref I J K L Kphi n Phi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.0 18 * c_ n3n_ * 0.0500 3 0.

#out_of_plane cvff_auto

E = Kchi * [ 1 + cos(n*Chi - Chi0) ]

!Ver Ref I J K L Kchi n Chi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.0 18 * c'_ * * 10.0000 2 180.0000

#nonbond(12-6) cvff

@type A-B
@Combination geometric

E = Aij/r^12 - Bij/r^6
where Aij = sqrt( Ai * Aj )
Bij = sqrt( Bi * Bj )

!Ver Ref I A B
!---- --- ---- ----------- -----------
1.0 1 st 12.3645 0.00954
1.0 1 ao 196.1446 0.03230
1.0 1 at 12.3645 0.00954
1.0 1 mgo 1636.3265 0.07688
1.0 1 mgh 1636.3265 0.07688
1.0 1 cao 17814.73 0.5987
1.0 1 cah 17624.076 0.595
1.0 1 feo 702.54 0.0504
1.0 1 lio 112.01 0.0201
1.0 1 ob 629358.0000 625.50000
1.0 1 obss 629358.0000 625.50000
1.0 1 obts 629358.0000 625.50000
1.0 1 obos 629358.0000 625.50000
1.0 1 ohs 629358.0000 625.50000
1.0 1 oh 629358.0000 625.50000
1.0 1 oh- 629358.0000 625.50000
1.0 1 o* 629358.0000 625.50000
1.0 1 ho 0.00000001 0.00000
1.0 1 h* 0.00000001 0.00000
1.0 1 Na 14763.1719 87.65132
1.0 1 K 754506.86 549.37
1.0 1 Cs 3998193.96 1264.63
1.0 1 Ca 125966.6068 224.46969
1.0 1 Ba 1799606.56 582.25
1.0 1 Mg 1369.00 69.22
1.0 1 Sr 1185860.37 688.73
1.0 1 Pb 861150.71 638.08
1.0 1 Cl 21081006.97 2905.31

#bond_increments cvff

!Ver Ref I J DeltaIJ DeltaJI
!---- --- ---- ---- ------- -------
2.3 23 no o- 0.1684 -0.1684

[franzlang]

the original CLAYFF paper is J. Phys. Chem. B 2004, 108, 4, 1255–1266 (https://doi.org/10.1021/jp0363287)

[iermi]

Those are the typical forcefield files. The first part is describing atom types with connectivities between them and charges. Then when it goes to bonds, angles and dihedrals it specifies atom types which are forming those things and the constants (parameters for respective potentials). What you basically can learn from that is that not every oxygen is the same, not every hydrogen is the same etc. The first one is important to know when you create a starting structure and assign atom types. Other parts for bonds, angles and dihedrals are essential to know it they are exist for things which you have created. If a parameter is missing it has to be derived, because the simulation won't start without parameters. The similar idea about non-bonded parameters (for atoms which are not connected by a chemical bond).