Input and Output

Typical usages of I/O functions for MD files are shown in belows.

PDB files

# read pdb data and generate a new variable t whose type is TrjArray
t = mdload("protein.pdb")

# after some editings
mdsave("protein_edited.pdb", t)

AMBER files

AMBER NetCDF trajectory file

# pdb files can be used for obtaining topology information which is used in atom selections
t = mdload("run.pdb")

# read AMBER NetCDF data and generate a new variable t whose type is TrjArray
# the topology information can be attached by the option `top=t`
t = mdload("run.nc", top=t)

# after some calculations
mdsave("run_edited.nc", t)

CHARMM/NAMD files

# read PSf data and generate a new variable t whose type is TrjArray
# Although PSF file does not contain coordinates, topology information is used in atom selections
t = mdload("run.psf")
# or if you don't have PSF files, pdb can be used to obtain topology information
t = mdload("run.pdb")

# read dcd file and generate a new variable t whose type is TrjArray
# the topology information can be attached by the option `top=t`
t = mdload("run.dcd", top=t)
# after some calculations
mdsave("run_edit.dcd", t)

GROMACS files

not available yet