14. Trajectory Converters
Below is the list of converters present in MDANSE. These allow for the outputs of a variety of MD simulation software to be able to be used in MDANSE by converting the various file formats to MMTK NetCDF format that can be used by MDANSE. All converters convert the positions and other vital values such as unit cell parameters, but velocities and forces are converted by only select converters.
Each converter requires different things to work and provides different options. This is detailed in the sections below. The only things that all converter windows have in common are the buttons (described in main text) and the output files field. At the beginning, that is just as the converter window is opened, this field will appear as follows:
Output files
Format: string
Default: ~\output.nc (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the MD file except velocities.
However, once an input file is selected (that is, Browse button next to an input file field is clicked, a file is selected in the file browser, and OK is clicked), MDANSE tries to generate a useful file name and place it in the same folder as the input file. Therefore, the output file field will appear as follows:
Output files
Format: string
Default: original_trajectory_directory_path\original_trajectory_file_name (where original_trajectory_directory_path is the path where the trajectory being converted is located, and original_trajectory_file_name is the name of the trajectory being converted)
Also, (n) may be appended to the end of the proposed file name if a file with the initial name already exists, where n is the lowest number for which a file does not exist.
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the MD file except velocities.
14.1. CASTEP converter
MDANSE can convert .md files generated by CAmbridge Serial Total Energy Package (CASTEP) [Ref27] of any version, and the header can be of any length. The converter expects velocities and forces to be written in the MD file. Clicking on the CASTEP button brings up this window:
castep file
Format: string
Default: ..\..\..\Data\Trajectories\CASTEP\PBAnew.md
Description: the path to an MD file that contains the trajectory. The Browse button can be used to search for the file using the file browser.
Output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the MD file except velocities.
14.2. CHARMM converter
This converter allows the conversion from a trajectory generated with Chemistry at HARvard Macromolecular Mechanics (CHARMM) [Ref28]. Selecting CHARMM button will open the following window:
pdb file
Format: string
Default: ..\..\..\Data\Trajectories\CHARMM\2vb1.pdb
Description: a PDB file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory. If you do not have a PDB file, you can generate it in many ways, such as by using ‘gmx editconf’ Gromacs command.
Please note, however, that there are multiple ‘versions’ of PDB files, but MDANSE is quite strict regarding which ones it can read. Therefore, it is best to make sure the PDB complies with the specification in Ref [Ref29]. Notably, the terminal oxygens on the carboxylic acid end must be noted as OT1 and OT2; O1 and O2 will result in an obscure error.
dcd file
Format: string
Default: ..\..\..\Data\Trajectories\CHARMM\2vb1.dcd
Description: the CHARMM DCD trajectory file that stores the trajectory frames.
Time step (ps)
Format: strictly positive float
Default: 1.0
Description: the time step in picoseconds between two consecutive frames of CHARMM trajectory.
Fold coordinates in to box
Format: bool
Default: False
Description: <insert>
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the PDB and DCD files except velocities.
14.3. CP2K converter
This converter allows the conversion from a trajectory generated with CP2K [Ref43]. Selecting CP2K button will open a window with the following input fields:
pos file
Format: string
Default: ../../../Data/Trajectories/CP2K/p1-supercell-pos-ejemplo.xyz
Description: an XYZ output file containing the atom positions for every step of the simulation.
vel file
Format: string
Default: ../../../Data/Trajectories/CP2K/p1-supercell-vel-ejemplo.xyz
Description: an XYZ output file containing atom velocities for every step of the simulation.
This input is optional, as MDANSE can create approximate velocities of atoms based on their positions.
cell file
Format: string
Default: ../../../Data/Trajectories/CP2K/p1-supercell-1.cell
Description: an output file containing the dimensions of the simulation unit cell for each frame of the simulation.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the input files.
14.4. DFTB converter
Converts trajectories generated using software based on the Density Functional based Tight Binding (DFTB) method [Ref30]. It should work with all the related software, but if you have any issues, please let us know.
Selecting DFTB will open this window:
xtd file
Format: string
Default: ..\..\..\Data\Trajectories\Forcite\nylon66_rho100_500K_v300K.xtd
Description: a XTD file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory.
trj file
Format: string
Default: ..\..\..\Data\Trajectories\Forcite\nylon66_rho100_500K_v300K.trj
Description: the DFTB TRJ trajectory file that stores the trajectory frames.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the XTD and TRJ files except velocities.
14.5. Discover converter
This converter allows the conversion from a trajectory generated with Materials Studio [Ref31] Discover module to a MMTK NetCDF trajectory. It converts velocities but not forces. Clicking on Discover button will open this window:
xtd file
Format: string
Default: ..\..\..\Data\Trajectories\Discover\sushi.xtd
Description: a XTD file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory.
his file
Format: string
Default: ..\..\..\Data\Trajectories\Discover\sushi.his
Description: the Discover HIS trajectory file that stores the trajectory frames.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the XTD and HIS files except velocities.
14.6. DL_POLY converter
This converter allows the conversion from a trajectory generated with DL POLY [Ref32] to a MMTK NetCDF trajectory. It can convert both velocities and forces. Pressing the DL-POLY button will open this window:
field file
Format: string
Default: ..\..\..\Data\Trajectories\DL_POLY\FIELD_cumen
Description: the DL POLY FIELD file that stores the information about the system. This file is necessary to build up the MMTK universe related to the MMTK trajectory.
history file
Format: string
Default: ..\..\..\Data\Trajectories\DL_POLY\HISTORY_cumen
Description: the DL POLY HISTORY file that stores the trajectory frames.
atom aliases
Format: string
Default: {}
Description: MDANSE will create the MMTK universe with the atom names specified in the FIELD file. By default, MDANSE will interpret these names directly as if they were a chemical symbol. If this fails, MDANSE will remove the last character until it corresponds to a known chemical symbol. For example, an atom defined in the FIELD file as CB, will first be interpreted as an atom of chemical symbol CB. As it does not exist, MDANSE will interpret it as an atom of chemical symbol C, namely a carbon atom. Using this procedure, it can happen that some atom names can be misunderstood, or event not understood at all by MMTK. For example, aromatic carbons (CA) can be interpreted as calcium.
The aim of the Special atoms field is precisely to avoid such problems. The format for the Special atoms field is
{atom_name1:element1 <sep> atom_name2:element2 etc.}
where <sep> can be a white space, a comma, or a semicolon. In the example showed in figure 4.7, the string CS:C should be entered in the Special atoms field. Interestingly, the Special atoms field can also be used to specify united atoms. The syntax is exactly the same but, in that case, the element name must be replaced by the MMTK united atom code (e.g. CH3, CH2, CH, NH, NH2, NH3, OH, SH, etc.)
version
Format: int
Default: 2
Description: The version of DL POLY software. Different versions format the HISTORY file differently, so it is necessary to select the correct format.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the FIELD and HISTORY files.
14.7. DMol converter
This converter allows the conversion from a trajectory generated with Materials Studio [Ref31] DMol module to a MMTK NetCDF trajectory. Clicking on DMol button will open this window:
xtd file
Format: string
Default: ..\..\..\Data\Trajectories\Discover\sushi.xtd
Description: an XTD file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory.
his file
Format: string
Default: ..\..\..\Data\Trajectories\Discover\sushi.his
Description: the DMol HIS trajectory file that stores the trajectory frames.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the XTD and HIS files except velocities.
14.8. Forcite converter
This converter allows for the conversion from a trajectory generated with Materials Studio [Ref31] Forcite module to a MMTK NetCDF trajectory. It can convert both velocities and forces, if present. Clicking on DMol button will open this window:
xtd file
Format: string
Default: ..\..\..\Data\Trajectories\Forcite\nylon66_rho100_500K_v300K.xtd
Description: a XTD file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory.
trj file
Format: string
Default: ..\..\..\Data\Trajectories\Forcite\nylon66_rho100_500K_v300K.trj
Description: the Forcite TRJ trajectory file that stores the trajectory frames.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the XTD and HIS files except velocities.
14.9. Generic converter
Converts a trajectory written in ASCII to an MMTK NetCDF file, including both velocities and forces if present. This is useful if you have a trajectory from a software not currently supported by MDANSE. An example of such ASCII file can be found by clicking on Help in the window that appears when Generic is selected:
gt file
Format: string
Default: ..\..\..\Data\Trajectories\Generic\test.gt
Description: path to an ASCII trajectory file that will be converted to MMTK NetCDF format.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the XTD and HIS files except velocities.
14.10. Gromacs converter
Converts a trajectory generated by the Gromacs software [Ref33] into MMTK NetCDF format. A PDF file containing the data about the initial configuration must be provided, along with a trajectory in either an XTC, or, since version 1.6.0, a TRR format. The latter format supports velocity reading. Selecting Gromacs opens the following window:
pdb file
Format: string
Default: ..\..\..\Data\Trajectories\Gromacs\md.pdb
Description: a PDB file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory. If you do not have a PDB file, you can generate it in many ways, such as by using ‘gmx editconf’ Gromacs command.
Please note, however, that there are multiple ‘versions’ of PDB files, but MDANSE is quite strict regarding which ones it can read. Therefore, it is best to make sure the PDB complies with the specification in Ref [Ref29]. Notably, the terminal oxygens on the carboxylic acid end must be noted as OT1 and OT2; O1 and O2 will result in an obscure error.
xtc or trr file
Format: string
Default: ..\..\..\Data\Trajectories\Gromacs\md.xtc
Description: the Gromacs XTC or TRR trajectory file that stores the trajectory frames.
Fold coordinates in to box
Format: bool
Default: False
Description: <insert>
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the PDB and DCD files except velocities.
14.11. LAMMPS converter
Converts trajectories generated by Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [Ref34] into MMTK NetCDF format. Selecting LAMMPS opens the following window:
LAMMPS configuration file
Format: string
Default: ..\..\..\Data\Trajectories\LAMMPS\glycyl_L_alanine_charmm.config
Description: LAMMPS configuration file. It should contain box dimensions and the masses block.
LAMMPS trajectory file
Format: string
Default: ..\..\..\Data\Trajectories\LAMMPS\glycyl_L_alanine_charmm.config
Description: a .lammps file that stores the trajectory frames.
mass tolerance (uma)
Format: float
Default: 0.001
Description: For LAMMPS trajectories, the parameter used to identify the chemical elements present in the simulated system is the mass. MDANSE compares the values present in the “Masses” block in the LAMMPS configuration file with those stored in MDANSE’s own database and identify an element when both agree between the mass tolerance (the other input parameter available in the conversion interface). Naturally the masses appearing in the configuration file should be close to those in the database, but they are not necessarily the same. For example, the mass for hydrogen in the database is 1.0079 uma, but you could have a simulation done with a mass value of 1.008 or 1.01 or even just 1.
A possible solution may be to change the mass tolerance given using this option. However, as the MDANSE database contains the masses of all the isotopes, if the tolerance is such that more than one isotope can be assigned, the converter will also fail. Therefore, the safest solution is to check the values of the masses in the MDANSE database and modify the LAMMPS configuration file to use the same masses.
smart mass association
Format: bool
Default: True
Description: If this is set to True and there are two or more elements in the MDANSE database within the tolerance of the LAMMPS mass (ie. If there is more than one match), MDANSE will not fail with an error but instead match the element from the database that most closely matches the mass in the LAMMPS .config file.
Time step (fs)
Format: strictly positive float
Default: 1.0
Description: the time step in femtoseconds between two consecutive frames of the LAMMPS trajectory.
Number of time steps
Format: strictly positive int
Default: 0
Description: the number of steps you want to convert. If this is set to 0, MDANSE will convert all the frames in the trajectory.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the PDB and DCD files except velocities.
14.12. NAMD converter
Converts a trajectory generated with NAnoscale Molecular Dynamics (NAMD) [Ref35] to an MMTK NetCDF trajectory. Selecting NAMD opens the following window:
pdb file
Format: string
Default: ..\..\..\Data\Trajectories\CHARMM\2vb1.pdb
Description: a PDB file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory.
Please note, however, that there are multiple ‘versions’ of PDB files, but MDANSE is quite strict regarding which ones it can read. Therefore, it is best to make sure the PDB complies with the specification in Ref [Ref29]. Notably, the terminal oxygens on the carboxylic acid end must be noted as OT1 and OT2; O1 and O2 will result in an obscure error.
dcd file
Format: string
Default: ..\..\..\Data\Trajectories\CHARMM\2vb1.dcd
Description: the NAMD DCD trajectory file that stores the trajectory frames.
Time step (ps)
Format: strictly positive float
Default: 1.0
Description: the time step in picoseconds between two consecutive frames of CHARMM trajectory.
Fold coordinates in to box
Format: bool
Default: False
Description: <insert>
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the PDB and DCD files except velocities.
14.13. PDB converter
MDANSE can convert standalone PDB files into MMTK NetCDF. However, of the variety of PDB format, MMTK is capable of parsing only some; to ensure that a PDB can be read, it should comply with the specification in Ref [Ref29]. To do that, select PDB, and the following window will open:
pdb file
Format: string
Default: ..\..\..\Data\Trajectories\CHARMM\2vb1.pdb
Description: a PDB file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory. If you do not have a PDB file, you can generate it in many ways, such as by using ‘gmx editconf’ Gromacs command.
Please note, however, that there are multiple ‘versions’ of PDB files, but MDANSE is quite strict regarding which ones it can read. Therefore, it is best to make sure the PDB complies with the specification in Ref [Ref29]. Notably, the terminal oxygens on the carboxylic acid end must be noted as OT1 and OT2; O1 and O2 will result in an obscure error.
nb frame
Format: int int int
Default: 0 2 1
Description: The selection of frames that will be converted. The frames specified in both ‘from’ and ‘to’ are included (ie. by default frames 0, 1, and 2 are converted). The ‘by step of’ field specifies the periodicity of which frames are skipped, ie. if it is 1, every frame is converted, if it is 2, every other is converted, etc.
Time step (ps)
Format: strictly positive float
Default: 1.0
Description: the time step in picoseconds between two consecutive frames of CHARMM trajectory.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the PDB file except velocities.
14.14. VASP converter
Converts a trajectory generated with Vienna Ab-initio Simulation Package (VASP) to an MMTK NetCDF trajectory. Only trajectories created with VASP version 5 or higher can be converted. Selecting VASP opens the following window:
xdatcar file
Format: string
Default: ..\..\..\Data\Trajectories\VASP\XDATCAR_version5
Description: an XDATCAR file storing a trajectory.
Time step (ps)
Format: strictly positive float
Default: 1.0
Description: the time step in picoseconds between two consecutive frames of CHARMM trajectory.
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the PDB file except velocities.
14.15. XPLOR converter
Converts a trajectory generated by X-PLOR into the MMTK NetCDF format. Selecting XPLOR opens the following window:
pdb file
Format: string
Default: ..\..\..\Data\Trajectories\CHARMM\2vb1.pdb
Description: a PDB file of the system must be provided for the conversion. This file is necessary to build up the MMTK universe related to the MMTK trajectory.
Please note, however, that there are multiple ‘versions’ of PDB files, but MDANSE is quite strict regarding which ones it can read. Therefore, it is best to make sure the PDB complies with the specification in Ref [Ref29]. Notably, the terminal oxygens on the carboxylic acid end must be noted as OT1 and OT2; O1 and O2 will result in an obscure error.
dcd file
Format: string
Default: ..\..\..\Data\Trajectories\CHARMM\2vb1.dcd
Description: an X-PLOR DCD trajectory file that stores the trajectory frames.
Time step (ps)
Format: strictly positive float
Default: 1.0
Description: the time step in picoseconds between two consecutive frames of CHARMM trajectory.
Fold coordinates in to box
Format: bool
Default: False
Description: <insert>
output files
Format: string
Default: ~\output_trajectory_conversion (where ~ is the home directory)
Description: the path to and name of the file that will be created in MMTK NetCDF format, containing all the information from the PDB and DCD files except velocities.