File Specifications¶
ParaMol Force Field (.ff) file¶
When manually defining the symmetries of terms belonging to specific force groups, the user should adhere to the mapping shown in the table below. This is of particular importance if .frcmod and .prmtop files are to be generated after a parametrization. If the user does not want to generate these files, these rules may be ignored. It is also worth mentioning that these starting letters may be followed by any combination of letters and numbers. For example, “B0”, “B9999” or “BABC” are all valid symmetry-groups for the HarmonicBondForce group.
Term Type |
Starting Letter(s) |
|---|---|
HarmonicBondForce |
B |
HarmonicAngleForce |
A |
PeriodicTorsionForce |
T |
NonbondedForce |
None |
Scaling14 |
SC |
No Symmetry |
X |
ParaMol Force Field file.¶
HarmonicBondForce 0
0 0 6 0.10860000 289365.44000000 0 0 X
1 1 7 0.10860000 289365.44000000 0 0 X
2 3 8 0.10860000 289365.44000000 0 0 X
3 4 9 0.10860000 289365.44000000 0 0 X
4 5 10 0.10860000 289365.44000000 0 0 X
5 11 12 0.10120000 338569.28000000 0 0 X
6 11 13 0.10120000 338569.28000000 0 0 X
7 0 1 0.13980000 385848.48000000 0 0 X
8 0 5 0.13980000 385848.48000000 0 0 X
9 1 2 0.13980000 385848.48000000 0 0 X
10 2 3 0.13980000 385848.48000000 0 0 X
11 2 11 0.13860000 349698.72000000 0 0 X
12 3 4 0.13980000 385848.48000000 0 0 X
13 4 5 0.13980000 385848.48000000 0 0 X
HarmonicAngleForce 1
0 0 1 7 2.09230160 403.33760000 0 0 X
1 0 5 10 2.09230160 403.33760000 0 0 X
2 1 0 6 2.09230160 403.33760000 0 0 X
3 2 1 7 2.09230160 403.33760000 0 0 X
4 2 3 8 2.09230160 403.33760000 0 0 X
5 2 11 12 2.02580453 405.01120000 0 0 X
6 2 11 13 2.02580453 405.01120000 0 0 X
7 3 4 9 2.09230160 403.33760000 0 0 X
8 4 3 8 2.09230160 403.33760000 0 0 X
9 4 5 10 2.09230160 403.33760000 0 0 X
10 5 0 6 2.09230160 403.33760000 0 0 X
11 5 4 9 2.09230160 403.33760000 0 0 X
12 12 11 13 2.00922390 335.55680000 0 0 X
13 0 1 2 2.09474507 557.30880000 0 0 X
14 0 5 4 2.09474507 557.30880000 0 0 X
15 1 0 5 2.09474507 557.30880000 0 0 X
16 1 2 3 2.09474507 557.30880000 0 0 X
17 1 2 11 2.11097664 571.53440000 0 0 X
18 2 3 4 2.09474507 557.30880000 0 0 X
19 3 2 11 2.11097664 571.53440000 0 0 X
20 3 4 5 2.09474507 557.30880000 0 0 X
PeriodicTorsionForce 2
0 0 5 4 9 2.00000000 3.14159400 15.16700000 0 0 0 X
1 1 0 5 10 2.00000000 3.14159400 15.16700000 0 0 0 X
2 1 2 3 8 2.00000000 3.14159400 15.16700000 0 0 0 X
3 1 2 11 12 2.00000000 3.14159400 4.39320000 0 0 0 X
4 1 2 11 13 2.00000000 3.14159400 4.39320000 0 0 0 X
5 6 0 1 2 2.00000000 3.14159400 15.16700000 0 0 0 X
6 2 3 4 9 2.00000000 3.14159400 15.16700000 0 0 0 X
7 3 2 1 7 2.00000000 3.14159400 15.16700000 0 0 0 X
8 3 2 11 12 2.00000000 3.14159400 4.39320000 0 0 0 X
9 3 2 11 13 2.00000000 3.14159400 4.39320000 0 0 0 X
10 3 4 5 10 2.00000000 3.14159400 15.16700000 0 0 0 X
11 6 0 5 4 2.00000000 3.14159400 15.16700000 0 0 0 X
12 5 0 1 7 2.00000000 3.14159400 15.16700000 0 0 0 X
13 5 4 3 8 2.00000000 3.14159400 15.16700000 0 0 0 X
14 6 0 1 7 2.00000000 3.14159400 15.16700000 0 0 0 X
15 6 0 5 10 2.00000000 3.14159400 15.16700000 0 0 0 X
16 7 1 2 11 2.00000000 3.14159400 15.16700000 0 0 0 X
17 8 3 2 11 2.00000000 3.14159400 15.16700000 0 0 0 X
18 8 3 4 9 2.00000000 3.14159400 15.16700000 0 0 0 X
19 9 4 5 10 2.00000000 3.14159400 15.16700000 0 0 0 X
20 6 0 5 1 2.00000000 3.14159400 4.60240000 0 0 0 X
21 0 2 1 7 2.00000000 3.14159400 4.60240000 0 0 0 X
22 2 4 3 8 2.00000000 3.14159400 4.60240000 0 0 0 X
23 3 5 4 9 2.00000000 3.14159400 4.60240000 0 0 0 X
24 0 4 5 10 2.00000000 3.14159400 4.60240000 0 0 0 X
25 2 12 11 13 2.00000000 3.14159400 4.60240000 0 0 0 X
26 0 1 2 3 2.00000000 3.14159400 15.16700000 0 0 0 X
27 0 1 2 11 2.00000000 3.14159400 15.16700000 0 0 0 X
28 0 5 4 3 2.00000000 3.14159400 15.16700000 0 0 0 X
29 1 0 5 4 2.00000000 3.14159400 15.16700000 0 0 0 X
30 1 2 3 4 2.00000000 3.14159400 15.16700000 0 0 0 X
31 5 0 1 2 2.00000000 3.14159400 15.16700000 0 0 0 X
32 2 3 4 5 2.00000000 3.14159400 15.16700000 0 0 0 X
33 4 3 2 11 2.00000000 3.14159400 15.16700000 0 0 0 X
34 1 3 2 11 2.00000000 3.14159400 4.60240000 0 0 0 X
NonbondedForce 3
0 0 -0.09300000 0.33996695 0.35982400 0 0 0 X
1 1 -0.19100000 0.33996695 0.35982400 0 0 0 X
2 2 0.13660000 0.33996695 0.35982400 0 0 0 X
3 3 -0.19100000 0.33996695 0.35982400 0 0 0 X
4 4 -0.09300000 0.33996695 0.35982400 0 0 0 X
5 5 -0.17300000 0.33996695 0.35982400 0 0 0 X
6 6 0.12900000 0.25996425 0.06276000 0 0 0 X
7 7 0.13000000 0.25996425 0.06276000 0 0 0 X
8 8 0.13000000 0.25996425 0.06276000 0 0 0 X
9 9 0.12900000 0.25996425 0.06276000 0 0 0 X
10 10 0.13100000 0.25996425 0.06276000 0 0 0 X
11 11 -0.81820000 0.32499985 0.71128000 0 0 0 X
12 12 0.38680000 0.10690785 0.06568880 0 0 0 X
13 13 0.38680000 0.10690785 0.06568880 0 0 0 X
Scaling14 3
0 0 9 0.83333333 0.50000000 0 0 X
1 1 10 0.83333333 0.50000000 0 0 X
2 1 8 0.83333333 0.50000000 0 0 X
3 1 12 0.83333333 0.50000000 0 0 X
4 1 13 0.83333333 0.50000000 0 0 X
5 6 2 0.83333333 0.50000000 0 0 X
6 2 9 0.83333333 0.50000000 0 0 X
7 3 7 0.83333333 0.50000000 0 0 X
8 3 12 0.83333333 0.50000000 0 0 X
9 3 13 0.83333333 0.50000000 0 0 X
10 3 10 0.83333333 0.50000000 0 0 X
11 6 4 0.83333333 0.50000000 0 0 X
12 5 7 0.83333333 0.50000000 0 0 X
13 5 8 0.83333333 0.50000000 0 0 X
14 6 7 0.83333333 0.50000000 0 0 X
15 6 10 0.83333333 0.50000000 0 0 X
16 7 11 0.83333333 0.50000000 0 0 X
17 8 11 0.83333333 0.50000000 0 0 X
18 8 9 0.83333333 0.50000000 0 0 X
19 9 10 0.83333333 0.50000000 0 0 X
20 0 3 0.83333333 0.50000000 0 0 X
21 0 11 0.83333333 0.50000000 0 0 X
22 1 4 0.83333333 0.50000000 0 0 X
23 5 2 0.83333333 0.50000000 0 0 X
24 4 11 0.83333333 0.50000000 0 0 X
END
NetCDF File Specification¶
This is a specification for the NetCDF 4 based store file format used by ParaMol.
NetCDF File that stores system data such as coordinates, energies and forces.¶
netcdf paramol_data_sc_iter_40 {
dimensions:
n_structures = 4000 ;
n_atoms = 24 ;
spatial_dim = 3 ;
variables:
double reference_coordinates(n_structures, n_atoms, spatial_dim) ;
reference_coordinates:units = "nanometers" ;
double reference_forces(n_structures, n_atoms, spatial_dim) ;
reference_forces:units = "kilojoules/mol/nanometers" ;
double reference_energies(n_structures) ;
reference_energies:units = "kilojoules/mol" ;
// global attributes:
:_NCProperties = "version=1|netcdflibversion=4.4.1.1|hdf5libversion=1.10.1" ;
}