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 )

9. cut the trajectory in small subtrajectories according to information in an index file. This allows subsequent analysis of the subtrajectories that could, for example be the result of a cluster analysis. Use option -sub This assumes that the entries in the index file are frame numbers and dumps each group in the index file to a separate trajectory file.

10. select frames within a certain range of a quantity given in an .xvg file.

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). Atom number 1 of each molecule will be inside the box.

* com puts the center of mass of all residues

in the box. Not that this can break molecules that consist of more than one residue (e.g. proteins).

* inbox puts all the atoms in the box.

* nojump checks if atoms jump across the box and then puts them back. This has the effect that all molecules will remain whole (provided they were whole in the initial conformation), note that this ensures a continuous trajectory but molecules may diffuse out of the box. The starting configuration for this procedure is taken from the structure file, if one is supplied, otherwise it is the first frame.

* cluster clusters all the atoms in the selected index such that they are all closest to the center of mass of the cluster which is iteratively updated. Note that this will only give meaningful results if you in fact have a cluster. Luckily that can be checked afterwards using a trajectory viewer.

-pbc is ignored when -fit or -pfit is set, in that case molecules will be made whole.

Option -ur sets the unit cell representation for options

whole and inbox of -pbc All three options give different results for triclinc boxes and identical results for rectangular boxes.

rect is the ordinary brick shape.

tric is the triclinic unit cell.

compact puts all atoms at the closest distance from the center of the box. This can be useful for visualizing e.g. truncated octahedrons. The center for options tric and compact

is tric (see below), unless the option -center

is set differently.

Option -center centers the system in the box. The user can select the group which is used to determine the geometrical center. The center options are:

tric : half of the sum of the box vectors,

rect : half of the box diagonal,

zero : zero. Use option -pbc whole in addition to -center when you want all molecules in the box after the centering.

With -dt it is possible to reduce the number of frames in the output. This option relies on the accuracy of the times in your input trajectory, so if these are inaccurate use the

-timestep option to modify the time (this can be done simultaneously). For making smooth movies the program g_filter

can reduce the number of frames while using low-pass frequency filtering, this reduces aliasing of high frequency motions.

Using -trunc trjconv can truncate .trj in place, i.e. without copying the file. This is useful when a run has crashed during disk I/O (one more disk full), or when two contiguous trajectories must be concatenated without have double frames.

trjcat is more suitable for concatenating trajectory files.

Option -dump can be used to extract a frame at or near one specific time from your trajectory.

Option -drop reads an .xvg file with times and values. When options -dropunder and/or -dropover are set, frames with a value below and above the value of the respective options will not be written.

FILES

-f traj.xtc Input

Generic trajectory: xtc trr trj gro g96 pdb

-o trajout.xtc Output

Generic trajectory: xtc trr trj gro g96 pdb

-s topol.tpr Input, Opt.

Structure+mass(db): tpr tpb tpa gro g96 pdb xml

-n index.ndx Input, Opt.

Index file

-fr frames.ndx Input, Opt.

Index file

-sub cluster.ndx Input, Opt.

Index file

-drop drop.xvg Input, Opt.

xvgr/xmgr file

OTHER OPTIONS

-[no]h no

Print help info and quit

-nice int 19

Set the nicelevel

-b time 0

First frame (ps) to read from trajectory

-e time 0

Last frame (ps) to read from trajectory

-tu enum ps

Time unit: ps , fs , ns , us , ms , s , m or h

-[no]w no

View output xvg, xpm, eps and pdb files

-[no]xvgr yes

Add specific codes (legends etc.) in the output xvg files for the

xmgrace program

-skip int 1

Only write every nr-th frame

-dt time 0

Only write frame when t MOD dt = first time (ps)

-dump time -1

Dump frame nearest specified time (ps)

-t0 time 0

Starting time (ps) (default: don't change)

-timestep time 0

Change time step between input frames (ps)

-pbc enum none

PBC treatment (see help text for full description): none , whole ,

inbox , nojump , cluster or com

-ur enum rect

Unit-cell representation: rect , tric or compact

-center enum no

Center atoms in box: no , tric , rect or zero

-box vector 0 0 0

Size for new cubic box (default: read from input)

-shift vector 0 0 0

All coordinates will be shifted by framenr*shift

-fit enum none

Fit molecule to ref structure in the structure file: none , rot+trans

, translation or progressive

-ndec int 3

Precision for .xtc and .gro writing in number of decimal places

-[no]vel yes

Read and write velocities if possible

-[no]force no

Read and write forces if possible

-trunc time -1

Truncate input trj file after this time (ps)

-exec string

Execute command for every output frame with the frame number as argu

ment

-[no]app no

Append output

-split time 0

Start writing new file when t MOD split = first time (ps)

-[no]sep no

Write each frame to a separate .gro, .g96 or .pdb file

-[no]ter no

Use 'TER' in pdb file as end of frame in stead of default 'ENDMDL'

-dropunder real 0

Drop all frames below this value

-dropover real 0

Drop all frames above this value

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.

Mon 29 Aug 2005 trjconv(1)