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.