Topology file format¶
Nonbonded potentials¶
Lennard-Jones¶
\[U(r_{ij}) = 4\epsilon\left [ \left ( \frac{\sigma}{r_{ij}} \right)^{12} - \left ( \frac{\sigma}{r_{ij}} \right)^6 \right ]\]
Tabulated (conversion)¶
The appropriate table is selected, based on current chemical conversion.
Tabulated (mixed, conversion)¶
Arithmetic mixing of two tabulated potentials
Input
- tab1: first tabulated potential
- tab2: second tabulated potential
- type: the type of particles to count in order to calculate conversion
- total_number: the total expected number of particles of given type M
The conversion is defined as:
\[\Phi = \frac{N_{type}}{M}\]
And the effective potential:
\[U(r_{ij}) = \Phi U^{tab1} + (1-\Phi) U^{tab2}\]
Bonded potentials¶
Harmonic bond¶
\[U(r) = \frac{1}{2}K(r-r_0)^2\]
FENE bond¶
\[U(r) = -\frac{1}{2} K b^2 log \left( 1 - \frac{r^2}{b^2} \right)\]
FENE bond with LJ interactions included¶
\[U(r) = -\frac{1}{2} K b^2 log \left( 1 - \frac{r^2}{b^2} \right) + 4\epsilon\left [ \left ( \frac{\sigma}{r_{ij}} \right)^{12} - \left ( \frac{\sigma}{r_{ij}} \right)^6 \right ]\]
Harmonic angle¶
\[U(\theta) = \frac{1}{2} K(\theta - \theta_0)^2\]
Cosine angle¶
\[U(\theta) = \frac{1}{2} K(1.0 + cos(\theta - \theta_0))\]
Harmonic n-cosine dihedral¶
\[U(\phi) = K(1 + cos(multiplicity*\phi - \phi_0));\]
Ryckaert Bellemans dihedral¶
\[U(\phi) = \sum^{5}_{n=0} K_n cos^n(\phi)\]
Dihedral Harmonic¶
\[U(\phi) = \frac{1}{2} K (\phi - \phi_0)^2\]
Topology file¶
In principle, ChemLab uses GROMACS-like topology file format. However, some functional types are different.
[ bondtypes ]¶
| Name of interaction | func | params |
|---|---|---|
| Harmonic eq1 | 1 | r0, K [1] |
| FENE eqFENE | 7 | b, K [1] |
| Tabulated | 8 | table index [2] |
| FENE + LJ eqFENELJ | 9 | b, K, sigma, epsilon |
| [1] | (1, 2) Force constant internally divided by 2.0 |
[ angletypes ]¶
| Name of interaction | func | params |
|---|---|---|
| Harmonic eq2 | 1 | theta0 (deg), K [2] |
| Tabulated | 8 | table index |
| Cosine eq3 | 11 | theta0 (deg), K [2] |
| [2] | (1, 2, 3) Force constant internally divided by 2.0 |
[ dihedraltypes ]¶
| Name of interaction | func | params |
|---|---|---|
| HarmonicNCos eq4 | 1 | phi0 (deg), K, multiplicity |
| Ryckaert Bellemans eq5 | 3 | K0, K1, K2, K3, K4, K5 |
| Tabulated | 8 | table index |
| Harmonic eq7 | 12 | phi0 (deg), K |
[ nonbond_params ]¶
Every line should follow the format
T1 T2 func <params>
where T1, T2 are atom types, func defines the type of non-bonded interaction and params is the set of parameters. We show the list of currently available non-bonded interactions with the corresponding parameters in the table below.
| Name of interaction | func | params |
|---|---|---|
| Lennard-Jones lj | 1 | sigma [3], epsilon [3] |
| Tabulated | 8 | filename [4] |
| Tabulated (conversion) tc | 9 | filename*, type, total number, p_min, p_max, is_default* |
| Tabulated (mixed, conversion) | 10 | tab1, tab2, type, total_number |
| Tabulated scaled by lambda | 11 | filename*, max_force* |
| Tabulated (mixed, static) | 12 | tab1, tab2, mix value |
| Tabulated (cap radius) | 13 | filename, cap radius |
| Tabulated (scaled pairs) | 14 | filename, scale increment, max_force* |
| Lennard-Jones scaled by lambda | 15 | sigma*, epsilon*, max_force* |
| Lennard-Jones capped | 16 | sigma*, epsilon*, cap radius |
| Tabulated (multi mixed) | 17 | type, total number, p_min:p_max:table1:table2, p_min:p_max:table1:table2, p_min:p_max:table1:table2, … |
| Tabulated (scaled pairs from file) ts_ | 18 | tab filename, pair list filename, scaling factor (default: 0.0) |
Footnotes
| [3] | (1, 2) If not set then the values are taken from the included force-field. |
| [4] | if the filename is not given then it will be constructed from atom type names: ‘table_T1_T2.xvg’ where T1, T2 are |
type names.