Input/output files:

Input files:

*Main input

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

*Trajectory

The high-resolution trajectory in one of the following formats:

XTC

¹- Compressed binary trajectory format used in GROMACS and LAMMPS. This is the recommended format.

TRR

¹- Binary trajectory format used in GROMACS.

XMOL

- Text-based XYZ trajectory format [XMOL]*.xmol, or a set of numerated files as for option MDYN below.

PDB

- Text-based trajectory format *.pdb

MDYN

- 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

It is assumed that in all cases, the atoms and molecules are arranged in the standard 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).

Output files:

CG trajectory

in XMOL or XTC¹format.

CG molecular types descriptions

in [MMOL].mmol format, but without bonds: *.CG.mmol.

Run:

cgtraj cgtraj.inp