Output Files

The following output files are printed by PQ. The individual file names can be changed via the corresponding MD Output File Keys in the .in file. Alternatively, a common prefix for all output files can be provided using the file_prefix key.

All data blocks shown for a single simulation step or frame are concatenated without blank lines in the output files.

Box File

File Type: .box

Contains the three lattice parameters (a, b, c) and the three angles (α, β, γ) of the simulation box for every frame in the following format:

step_number a b c α β γ

The lattice parameters are given in units of Å and the angles are given in units of degrees.

Charge File

File Type: .chrg

Stores the charge of each atom for every frame of the simulation in the following format:

line 1: n_atoms a b c α β γ

line 2: empty

line 3 to (n_atoms + 2): atom_type_name charge

The parameters n_atoms, a, b, c, α, β, and γ in the first line of every frame denote the number of atoms in the simulation box and the respective box parameters in units of Å and degrees. The second line is left empty. The following lines contain the name of the atom type (as given in the Moldescriptor file) and its charge in units of the elementary charge e for each atom in the system.

Energy File

File Type: .en

Stores information about the energy and various other quantities of the system for every frame in the following format:

step_number T P E_tot E_QM N_QM-atoms E_kin E_intra E_Coulomb E_non-Coulomb E_bond E_angle E_dihedral E_improper V ρ E_p-NH E_χ-NH r_lower r_upper p looptime

Quantity	Description	Unit	Printed
step_number	overall number of simulation steps so far	-	A
T	temperature	K	A
P	pressure	bar	A
Etot	total energy	kcal/mol	A
EQM	quantum mechanical energy	kcal/mol	QM
NQM-atoms	number of atoms treated quantum mechanically	-	QM
Ekin	kinetic energy	kcal/mol	A
Eintra	MM intra-molecular energy	kcal/mol	A
ECoulomb	MM Coulomb energy	kcal/mol	MM
Enon-Coulomb	MM non-Coulomb energy	kcal/mol	MM
Ebond	total energy of the MM bonds	kcal/mol	MM*
Eangle	total energy of the MM angles	kcal/mol	MM*
Edihedral	total energy of the MM dihedrals	kcal/mol	MM*
Eimproper	total energy of the MM improper dihedrals	kcal/mol	MM*
V	volume	ų	P
ρ	density	g/cm³	P
Ep-NH	momentum energy of the Nose Hoover chain thermostat	kcal/mol	NH
Eχ-NH	friction energy of the Nose Hoover chain thermostat	kcal/mol	NH
rlower	lower bound of the distance constraints	Å	DC
rupper	upper bound of the distance constraints	Å	DC
p	total momentum	amu Å/fs	A
looptime	time taken to complete the full MD simulation step	s	A

Note

The last column of the table denotes when the respective quantity is printed to the .en file. The letters have the following meaning:

A: Always printed

QM: Only printed if QM atoms are present

MM: Only printed if MM atoms are present

MM*: Only printed if MM atoms are present, which are not treated by the GUFF File

P: Only printed if pressure coupling is enabled via the Pressure Coupling Keys in the .in file

NH: Only printed if the Nose Hoover chain thermostat is enabled via the Thermostat key in the .in file

DC: Only printed if distance constraints are applied

If the interval at which the results are printed to the output files is changed via the Output Frequency key in the .in file, the values in the .en file are averaged over the respective interval.

All printed quantities in correct ordering and with associated units are given in the .info output file, which is described in section Info File.

Force File

File Type: .force

Stores the force F acting on each atom for every frame of the simulation in the following format:

line 1: n_atoms a b c α β γ

line 2: total_force

line 3 to (n_atoms + 2): atom_type_name F_x F_y F_z

The parameters n_atoms, a, b, c, α, β, and γ in the first line of every frame denote the number of atoms in the simulation box and the respective box parameters in units of Å and degrees. The second line gives the total force acting on the system in \(\frac{\text{kcal}}{\text{mol Å}}\). The following lines contain the name of the atom type (as given in the Moldescriptor file) and the associated forces acting along the x, y and z direction in \(\frac{\text{kcal}}{\text{mol Å}}\) for each atom in the system.

Note

The total force should be marginal if no external fields (Planned) are applied to the system.

Info File

File Type: .info

Stores information about various quantities of the system and their units for the last frame calculated. The quantities are identical to those in the .en file (described under section Energy File), except the first entry which is the total simulation time in ps instead of the step number. Entries in the .info file are read from left to right and top to bottom.

Instant Energy File

File Type: .instant_en

Stores the exact same quantities as the .en file (described under section Energy File), but for the last frame calculated and not averaged over the interval set by the Output Frequency key in the .in file. Therefore, it is identical to the .en file if the output frequency is set to 1.

Log File

File Type: .log

Starts with general information about the PQ program, such as the author, version, and the date of compilation. The file then tracks the initialization of PQ and the simulation settings used. In case of a successful simulation, the file ends with the text ‘PQ ended normally’. In case of an error, the file shows the respective error message.

Momentum File

File Type: .mom

Stores the total momentum p and the total angular momentum L of the system as well as their individual x, y and z components for every frame in the following format:

step_number p p_x p_y p_z L L_x L_y L_z

The total momentum and its components are given in units of \(\frac{\text{amu Å}}{\text{fs}}\), while the total angular momentum and its components are given in units of \(\frac{\text{amu }\text{Å}^2}{\text{fs}}\).

Reference File

File Type: .log.ref

Lists the references to be cited when publishing results obtained via the chosen simulation settings as regular text and in BibTeX format.

Restart File

File Type: .rst

Stores the coordinates, velocities, and forces of each atom for the last performed simulation step in the following format:

line 1: “Step” step_number

line 2: “Box” a b c α β γ

line 3 to (n_atoms + 2): element running_index moltype x y z v_x v_y v_z F_x F_y F_z

The first line contains the string “Step” followed by the total number of performed simulation steps. The second line starts with the string “Box” followed by the parameters a, b, c, α, β, and γ, which denote the parameters of the simulation box in units of Å and degrees. The following lines contain the element symbol, a running index just for human readability, the moltype the atom belongs to according to the Moldescriptor setup file, the Cartesian coordinates in Å, the velocities in \(\frac{\text{Å}}{\text{fs}}\), and the forces in \(\frac{\text{kcal}}{\text{mol Å}}\) for each atom in the system. The moltype value is set to 0 if no Moldescriptor file is used.

Note

If the thermostat is set to the Nose Hoover chain via the Thermostat key in the .in file, as many additional lines as chosen number of heat baths (set via the NH-Chain Length key) are added to the restart file between the box and the atom information in the following format:

“Chi” level χ ζ

Every line associated with the Nose Hoover chain thermostat begins with the string “Chi” followed by the level of the thermostat, the corresponding friction coefficient χ and the cumulant ζ. Since these are time-dependent variables, they are printed to the restart file.

Attention

A .rst file needs to be provided by the user for the first run of the simulation alongside the Input File. Furthermore, this first .rst file has to contain all atoms of a moltype in the same order as provided in the Moldescriptor setup file. In this first .rst file, the whole first line denoting the step number as well as the columns denoting the velocities and forces can be omitted. If the parameters defining the box angles are left out, they are assumed to be 90°. Also the information about the Nose Hoover chain thermostat is not needed for the first .rst file and can be omitted. The whole line defining the box can be left out as well if the box is cubic and its density is provided via the Density keyword in the .in file.

Stress File

File Type: .stress

Stores the individual components of the stress tensor σ for every frame in the following format:

step_number σ_ax σ_ay σ_az σ_bx σ_by σ_bz σ_cx σ_cy σ_cz

The individual components of the stress tensor are given in units of \(\frac{\text{kcal}}{\text{mol Å}^3}\). The first character of the index denotes the lattice parameter (a, b, c), while the second character denotes the respective lattice parameter component (x, y, z).

Timing File

File Type: .timings

Tracks the time PQ takes for executing the individual parts of the simulation.

Trajectory File

File Type: .xyz

Stores the coordinates (x, y, z) of each atom for every frame of the simulation in the following format:

line 1: n_atoms a b c α β γ

line 2: empty

line 3 to (n_atoms + 2): atom_type_name x y z

The parameters n_atoms, a, b, c, α, β, and γ in the first line of every frame denote the number of atoms in the simulation box and the respective box parameters in units of Å and degrees. The second line is left empty. The following lines contain the name of the atom type (as given in the Moldescriptor file) and the associated Cartesian coordinates in Å for each atom in the system.

Velocity File

File Type: .vel

Stores the velocity v of each atom for every frame of the simulation in the following format:

line 1: n_atoms a b c α β γ

line 2: empty

line 3 to (n_atoms + 2): atom_type_name v_x v_y v_z

The parameters n_atoms, a, b, c, α, β, and γ in the first line of every frame denote the number of atoms in the simulation box and the respective box parameters in units of Å and degrees. The second line is left empty. The following lines contain the name of the atom type (as given in the Moldescriptor file) and the associated velocities along the x, y and z direction in \(\frac{\text{Å}}{\text{fs}}\) for each atom in the system.

Virial File

File Type: .vir

Stores the individual components of the virial tensor W for every frame in the following format:

step_number W_ax W_ay W_az W_bx W_by W_bz W_cx W_cy W_cz

The individual components of the virial tensor are given in units of \(\frac{\text{kcal}}{\text{mol}}\). The first character of the index denotes the lattice parameter (a, b, c), while the second character denotes the respective lattice parameter component (x, y, z).