Input File Specifications

The bulk of MPMC runs require two plain text files, the input script and the PQR data file. The input script contains all of the commands defining the type of run to be performed as well as details about the state point, control of the potentials, control of the input/output, etc. The PQR file contains the atomic positions of the system as well as force field parameters such as partial charges and van der Waals coefficients on each atom.

MPMC Input Script

The MPMC input script contains a series of commands, usually of the form [command name] [on|off|value], and one per line. Comments may be included by beginning a line with ! or #. Whitespace is ignored and the order of the commands is not important as the entire input script is read and then the simulation is started. A minimal MPMC input script contains the ensemble to simulate in, the temperature (and possibly pressure), the number of steps, and the output frequency. As an example, a minimal input script for a \(\mu VT\) simulation of H₂ sorption in MOF-5 is provided below and the full example is found in tutorial 1.

job_name MOF5+BSS

ensemble uvt

temperature 298.0
pressure    1.0

numsteps 100
corrtime 4

insert_probability 0.667

pqr_input input.pqr
abcbasis  25.669 25.669 25.669 90 90 90

The full list of commands is available in Commands.

PQR File

PQR files used by MPMC contain additional columns compared to standard .pqr or .pdb files to support inclusion of the force field parameters. The format is as follows:

1     2    3          4           5    6         7  8  9  10    11      12              13          14        15     16         17  18  19
ATOM  ID#  Element    MolecLabel  M/F  MolecID   x  y  z  mass  charge  polarizability  LJ epsilon  LJ sigma  Omega  GWP alpha  C6  C8  C10

1: ATOM verbatim

2: Atom ID, starting from 1 to N_atoms

3: Element label, doesn’t have to be unique, can include additional numbers/letters in the case of multiple atom types (e.g. “ZN”, “C1”, “O2”, “H2G”, etc)

4: Molecule label, doesn’t have to be unique (e.g. “MOF” or “H2”)

5: M = Movable, F = Frozen (determines whether a molecule has Monte Carlo moves applied to it, e.g. a solid porous material would be frozen and sorbate movable in typical simulations)

6: Molecule ID, starting from 1 to N_molecules

7-9: X, Y, Z cartesian coordinates in Angstroms

10: Mass of atom in amu

11: Partial charge in e

12: Polarizability in Angstrom³

13: \(\epsilon\) (in K) for Lennard-Jones simulations or \(\beta\) (in Angstrom^-1) for PHAHST simulations

14: \(\sigma\) (in Angstrom) for Lennard-Jones simulations or \(\rho\) (in Angstrom) for PHAHST simulations

15: \(\omega\) (in a.u.) for many-body van der Waals interactions

16: \(\alpha\) for gaussian wave packet Coulombic interactions (normally not needed)

17-19: Dispersion coefficients (in a.u.) for PHAHST simulations

For typical Lennard-Jones simulations columns 15-19 are not needed and if omitted will default to 0. An excerpt of the PQR file from the tutorial 2, BSSP H₂ sorption in MOF-5, is provided below as an example.

ATOM      1 ZN   MOF F   1       7.568   5.314  -7.516  65.3900   1.8530  0.16000 62.39930  2.46200
ATOM      2 ZN   MOF F   1       5.335  -5.287  -5.283  65.3900   1.8530  0.16000 62.39930  2.46200
ATOM      3 ZN   MOF F   1       5.335   7.547   7.551  65.3900   1.8530  0.16000 62.39930  2.46200
ATOM      4 ZN   MOF F   1       5.335  -7.520   7.551  65.3900   1.8530  0.16000 62.39930  2.46200
ATOM      5 ZN   MOF F   1      -5.266   7.547  -7.516  65.3900   1.8530  0.16000 62.39930  2.46200
[...]
ATOM    425 H2G  H2  M    2      0.000   0.000   0.000  0.00000 -0.74640  0.69380 12.76532  3.15528
ATOM    426 H2E  H2  M    2      0.371   0.000   0.000  1.00800  0.37320  0.00044  0.00000  0.00000
ATOM    427 H2E  H2  M    2     -0.371  -0.000   0.000  1.00800  0.37320  0.00044  0.00000  0.00000
ATOM    428 H2N  H2  M    2      0.363   0.000   0.000  0.00000  0.00000  0.00000  2.16726  2.37031
ATOM    429 H2N  H2  M    2     -0.363  -0.000   0.000  0.00000  0.00000  0.00000  2.16726  2.37031

Surface Fitting Files

The default surface fitting input consists of three Euler angles specifying the rotational configuration for each molecule in the dimer followed by a list of center-of-mass distances and their respective ab initio energies used in the fitting process. When using this style of surface fitting the input PQR file consists of the two molecules in the dimer with their center-of-mass at the origin. An example for CO₂ calculated at the CCSD(T)/CBS level is provided below:

* Data for slip parallel orientation of CO2 dimer

alpha1      0.3333333333 pi
beta1       0.0
gamma1      0.0

alpha2      0.3333333333 pi
beta2       0.0
gamma2      0.0

2.5  7911.3
2.6  5866.4
2.7  3581.48
2.8  2002.818
2.9  933.35671939
3.0  227.08190367
[...]

Surf_multi_fit Files

The surf_multi_fit inputs are more general, able to handle an arbitrary number of atoms or molecules in arbitrary configurations. They begin with the word “Configuration”, followed by the ab initio energy, then a list of atoms in the system, with the format: atom type, molecule number, x, y, z, and partial charge. An example for an He dimer is shown below:

Configuration 1
286570.1
He 1   0 0 0 0
He 2 0.529177 0 0 0
Configuration 2
173854.3
He 1   0 0 0 0
He 2 0.66147125 0 0 0
Configuration 3
104342.9
He 1   0 0 0 0
He 2 0.7937655 0 0 0
[...]