Input

• Geometry file in modified Tinker's *.xyz format
• File *.ff that contains forcefield parameters for given geometry

Geometry

Sample geometry file for single molecule of butane is shown here:

4 Butan # id name x y z bonds 1 C3 0 0 0 2 2 C2 1.5 0 0 3 3 C2 3.0 0 0 4 4 C3 4.5 0 0 0

First line contains number of atoms plus name of the system The next lines contain: serial numer of an atom its name that must contain information about an element associated with the atom three dimensional position of the atom indexes of atoms that are directly connected to current atom

Forcefield

Example (united-atom) forcefielf for butane can be written as follows:

# parameters for butane # united atom model # keyword atomname mass charge nr of neighbours comment atom C3 6.0 0.0 1 "sp3 carbon" atom C2 6.0 0.0 2 "sp2 carbon" # keyword atom list epsilon sigma vdw C2 C2 1.0 3.0 vdw C2 C3 1.0 3.0 vdw C3 C3 1.0 3.0 # keyword atom list k length bond C2 C2 1 1.7 bond C2 C3 1 1.7 # keyword atom list k angle angle C3 C2 C2 0 2 angle C2 C2 C2 0 2 # keyword atom list energy angle multiplicity torsion C3 C2 C2 C3 1 2 1

Note that atom types are recognized preciselly by its name. Every parameters that lacks are assumed to be zero, so if you need to have a system that interact by harmonic bonds only (no dispersion interaction) just comment out unneeded interactions

The following keywords for forcefield parameters are allowed:

atom

properties of single atom: mass, charge

vdw

parameters (epsilon and sigma) for long-range Van der Waals interactions. Pairs must be explicitelly mentioned

bond

harmonic bond interaction: force constant and equilibrium length of bond

angle

harmonic stretching of angle: force constant and equilibrium value of the angle in degrees

torsion

torsional angle with energy scale, angle value and multiplicity

Output

• *.pix files that contains configuration of a simulation as well as properties of the GUI: colors and window sizes. It can be further used to start again the simulation.
• first.xyz & last.xyz files that contains first and last frame of simulated system
• first.xyz.pdb & last.xyz.pdb equivalent of above files in Protein Data Bank format
• acc.dat contains actual values of some properties for every chosen simulation step
• str.dat contains histograms for structural quantities like pair correlation function and rdf averaged over chosen period of time