File formats

GROMACS
File Formats

Main Table of Contents

VERSION 3.2
Sun 25 Jan 2004

Parameter files mdp run parameters, input for grompp and tpbconv m2p input for xpm2ps

Structure files

gro: GROMACS format
g96: GROMOS-96 format
pdb: brookhaven Protein DataBank format
Generic structure formats: gro, g96, pdb, tpr, tpb or tpa
Structure+mass(db): tpr, tpb, tpa, gro, g96 or pdb.: Structure and mass input for analysis tools. When gro or pdb is used approximate masses will be read from the mass database.

Topology files

top: system topology (ascii)
itp: include topology (ascii)
rtp: residue topology (ascii)
ndx: index file

Run Input files

tpr: system topology, parameters, coordinates and velocities (binary, portable)
tpa: system topology, parameters, coordinates and velocities (ascii)
tpb: system topology, parameters, coordinates and velocities (binary)
Generic run input file formats: tpr, tpb or tpa

Trajectory files

trj: x, v and f (binary, full precision)
trr: x, v and f (binary, full precision, portable)
xtc: x only (compressed, portable, any precision)
g87: x and v (ascii)
gro: x and v (ascii, any precision)
g96: x only (ascii, fixed high precision)
pdb: x only (ascii, reduced precision)
Full precision formats: trr or trj
Generic trajectory formats: xtc, trr, trj, gro, g96, pdb or g87

Energy files

ene: energies, temperature, pressure, box size, density and virials (binary)
edr: energies, temperature, pressure, box size, density and virials (binary, portable)
Generic energy formats: edr or ene

Other files

dat: generic, preferred for input
edi: essential dynamics constraints input for mdrun
edo: essential dynamics constraints output for mdrun
eps: Encapsulated Postscript
log: log file
map: colormap input for do_dssp
mtx: binary matrix data
out: generic, preferred for output
tex: LaTeX input
xpm: ascii matrix data, use xpm2ps to convert to eps
xvg: xvgr input

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