General organization

TRANAL package consists of a number of utilities for analyzing of atom trajectories generated by molecular dynamics programs. The package is constructed to work mainly with MDynaMix molecular dynamics program, but is able to accept trajectories written in some other formats: trajectories written in XMOL format, PDB trajectories from GROMACS and NAMD binary trajectories.

It is supposed that in all cases, the atoms and molecules are arranged in the following way: (the same as in MDynaMix program):

<molecules of type 1><molecules of type 2>...

in each molecule type:

<molecule 1><molecules 2>...

in each molecule:

<atom1><atom2>... (the same atom order must be in all molecules of this type)

Additionally, a term ``site'' is determined. If one chooses one molecule of each type and set them one after another (in the same order as in the trajectory), then the number of each atom in this sequence would correspond to the ``site'' number.

Each of utilities in the TRANAL suite consists of two parts: the main block tranal_base.f, which reads trajectories, and a specific part which makes required analysis. Correspondingly, the input file for each utility consists of two parts: the first one which determines how to read trajectories, and the second part containing parameters for the required analysis.

Currently, the following analyzing utilities are included:

• bileldens - for membranes or bilayers: computation of mass density, electron density, and electrostatic potential across membrane

• diel - calculation of average dielectric permittivity

• diffus - calculation of the mean square displacement and the self-diffusion coefficients

• dryrun - just reading trajectories and optionally rewriting them to XMOL format

• latdiff - computation of 2D mean square displacement and lateral diffusion for membranes or bilayers

• order - computation of the order parameter and angular distribution of specific molecular vectors

• rdf - computation of radial distribution functions

• sdf - computation of spatial distribution functions

• torsion - computation of distributions of torsion angles

• torsion2 - Ramachandran plot for two torsion angles

• trtcf - computation of some time correlation functions

Each of utilities must be compiled by a Fortran compiler together with tranal_base block. For instance, the program for RDF calculations can be compiled by:

f77 -O3 -o rdf rdf.f tranal_base.f

Eventually, sizes of arrays may be needed to adjust, by editing tranal.h file, as well as sizes of arrays in each specific procedure.

Contributions for analysis of other properties are welcomed.