trjconv Main Table of Contents

VERSION 3.1 Thu 28 Feb 2002

Description

trjconv can convert trajectory files in many ways:
1. from one format to another
2. select a subset of atoms
3. remove periodicity from molecules
4. keep multimeric molecules together
5. center atoms in the box
6. fit atoms to reference structure
7. reduce the number of frames
8. change the timestamps of the frames (-t0 and -timestep)

The program trjcat can concatenate multiple trajectory files.

Currently seven formats are supported for input and output: .xtc, .trr, .trj, .gro, .g96, .pdb and .g87. The file formats are detected from the file extension. The precision of .xtc and .gro output is taken from the input file for .xtc, .gro and .pdb, and from the -ndec option for other input formats. The precision is always taken from -ndec, when this option is set. All other formats have fixed precision. .trr and .trj output can be single or double precision, depending on the precision of the trjconv binary. Note that velocities are only supported in .trr, .trj, .gro and .g96 files.

Option -app can be used to append output to an existing trajectory file. No checks are performed to ensure integrity of the resulting combined trajectory file.

Option -sep can be used to write every frame to a seperate .gro, .g96 or .pdb file, default all frames all written to one file. .pdb files with all frames concatenated can be viewed with rasmol -nmrpdb.

It is possible to select part of your trajectory and write it out to a new trajectory file in order to save disk space, e.g. for leaving out the water from a trajectory of a protein in water. ALWAYS put the original trajectory on tape! We recommend to use the portable .xtc format for your analysis to save disk space and to have portable files.

There are two options for fitting the trajectory to a reference either for essential dynamics analysis or for whatever. The first option is just plain fitting to a reference structure in the structure file, the second option is a progressive fit in which the first timeframe is fitted to the reference structure in the structure file to obtain and each subsequent timeframe is fitted to the previously fitted structure. This way a continuous trajectory is generated, which might not be the case when using the regular fit method, e.g. when your protein undergoes large conformational transitions.

Option -pbc sets the type of periodic boundary condition treatment. whole puts the atoms in the box and then makes broken molecules whole (a run input file is required).