MDCONVERT

NAME

mdconvert-mdtraj - use mdtraj to convert molecular dynamics trajectories between formats

DESCRIPTION

usage: mdconvert-mdtraj [-h] -o OUTPUT [-c CHUNK] [-f] [-s STRIDE] [-i INDEX]

[-a ATOM_INDICES] [-t TOPOLOGY] input [input ...]

Convert molecular dynamics trajectories between formats. The DCD, XTC, TRR, PDB, binpos, NetCDF, binpos, LH5, and HDF5 formats are supported (.dcd, .xtc, .trr, .binpos, .nc, .netcdf, .h5, .lh5, .pdb)

positional arguments:

input

path to one or more trajectory files. Multiple trajectories, if supplied, will be concatenated together in the output file in the order supplied. all of the trajectories should be in the same format. the format will be detected based on the file extension

required arguments:

-o OUTPUT, --output OUTPUT

path to the save the output. the output format will chosen based on the file extension (.dcd, .xtc, .trr, .binpos, .nc, .netcdf, .h5, .lh5, .pdb)

optional arguments:

-h, --help

show this help message and exit

-c CHUNK, --chunk CHUNK

number of frames to read in at once. this determines the memory requirements of this code. default=1000

-f, --force

force overwrite if output already exsits

-s STRIDE, --stride STRIDE

load only every stride-th frame from the input file(s), to subsample.

-i INDEX, --index INDEX

load a *specific* set of frames. flexible, but inefficient for a large trajectory. specify your selection using (pythonic) "slice notation" e.g. ’-i N’ to load the the Nth frame, ’-i -1’ will load the last frame, ’-i N:M to load frames N to M, etc. see http://bit.ly/143kloq for details on the notation

-a ATOM_INDICES, --atom_indices ATOM_INDICES

load only specific atoms from the input file(s). provide a path to file containing a space, tab or newline separated list of the (zero-based) integer indices corresponding to the atoms you wish to keep.

-t TOPOLOGY, --topology TOPOLOGY

path to a PDB/prmtop file. this will be used to parse the topology of the system. it’s optional, but useful. if specified, it enables you to output the coordinates of your dcd/xtc/trr/netcdf/binpos as a PDB file. If you’re converting *to* .h5, the topology will be stored inside the h5 file.