The force field

The general form of the force field implemented in the program is:

  $$U = U_{LJ} + U_{el} + U_{bond} + U_{ang} + U_{tors} + U_{impr}$$ (1)

where

  $$U_{LJ} = \sum_{non-bonded}4\varepsilon_{ij}\Big(\big(\frac{ \sigma_{ij}}{r_{ij}}\big)^{12}-\big(\frac{\sigma_{ij}}{r_{ij}}\big)^6\Big)$$ (2)

is the sum of Lennard-Jones interactions taken over non-bonded atom pairs. A pair of atoms is considered as non-bonded if they are on different molecules or if they are on the same molecule but separated by more than two covalent bonds. A case when a pair of atoms is separated by exactly 3 bonds (the so-called 1-4 neighbors) is treated separately, see below. $r_{ij}$ is the distance between atoms $i$ and $j$. Parameters $\varepsilon_{ij}$ and $sigma_{ij}$ for atom pair ($i,j$) are determined by default from the individual $\varepsilon_i$ and $\sigma_i$ parameters for atoms using combination rules; they can be also specified separately.

  $$U_{el} = \sum_{non-bonded}\frac{q_iq_j}{4\pi\epsilon_0r_{ij}}$$ (3)

is the sum of electrostatic interactions

The remaining terms in (1) are inramolecular interactions due to covalent bonds, covalent angles and torsion angles. They are described below.

For each molecule type used in the simulation a file describing molecular structure and parameters of the force field is needed. The file must have extension *.mmol . Some examples of .mmol files are given in moldb directory.

.mmol files consist of several parts which are described below. Lines, beginning with "#" are commentaries and they are ignored by the program. Other lines contain parameters in free format. The delimiter between keywords and parameters is one or more spaces. Do not use Tab as a delimiter, it may result in unpredictable behaviour.