Input/output files:

Input files:

*Trajectory

For reading trajectories, MagiC uses trajectory reading interface inhereted from http://www.fos.su.se/ sasha/mdynamix/MDynaMix molecular dynamics package. The following formats are supported:

XMOL

- Text-based XYZ trajectory format [XMOL]*.xmol.

PDB

- Text-based trajectory format http://www.rcsb.org/pdb *.pdb

MDYN

- (http://www.fos.su.se/ sasha/mdynamix/)MDynaMix trajectory binary format. It is usually given as a set of numerated files *.001,*.002, etc.

DCD

- CHARMM/NAMD binary trajectory file format: *.dcd

Each of these types of trajectory can be presented as a set of files with extentions *.001,*.002,*.003,...

It is supposed that in all cases, the atoms and molecules are arranged in the following way:

<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)

*Molecular type

descriptions for each type involved: [MMOL]*.mmol files (optional, see detailed description below).

*Main input

providing the mapping scheme, input trajectory and output files parameters.

Output files:

CG trajectory

in XMOL format.

CG molecular types descriptions

in [MMOL].mmol format, but without bonds: *.CG.mmol . They will be used at the next stage during RDFs calculations.

Run:

cgtraj cgtraj.inp