Atoms Input formats

There is 1 MCMD input file (in examples, named mcmd.inp). This is a simple text file with commands for the program. Possible commands are listed here.

There are 3 input formats for atoms:

1. Blank (no input file) -- valid for uVT ensemble simulations (e.g. filling an empty box to a thermodynamically reasonable density of gas)
2. XYZ format (input_atoms_xyz myfile.xyz), with columns as follows:

NOTE: The first line should contain the total number of atoms. The second line can contain anything, e.g. a comment. All atoms are assumed frozen for .xyz input. The 3rd and below lines are thus:

Column	Description	Example
1	Atom label -- 2-4 characters	Cu, H, O, CU1, OXY, CO1B
2	Cartesian coordinate in x direction, in Angstroms	0, 254, 3.138042
3	Cartesian coordinate in y direction, in Angstroms	1, -32, 5.280000
4	Cartesian coordinate in z direction, in Angstroms	14, 0.31, -13.41801
5	Partial charge on atom (in e) [optional]	0, -0.4231, 2.0

Example .xyz atoms input file (the first 4 atoms in MOF-5):

4

Zn  7.568   5.314   -7.516  1.85300
Zn  5.335   -5.287  -5.283  1.85300
Zn  5.335   7.547   7.551   1.85300
Zn  5.335   -7.520  7.551   1.85300

3. PDB format (input_atoms myfile.pdb), with columns as follows:

Column	Description	Example
1	"ATOM" verbatim.	ATOM
2	Atom ID number -- UNIQUE	1, 42, 200
3	Atom label -- 2-4 characters	Cu, H, O, CU1, OXY, CO1B
4	Molecule label -- 2-4 characters	MOF, H2O, CO2, ACE
5	Frozen or mobile marker (F atoms will be rigid during simulation)	F, M
6	Molecule ID number -- UNIQUE (for molecule)	1, 42, 200
7	Cartesian coordinate in x direction, in Angstroms	0, 254, 3.138042
8	Cartesian coordinate in y direction, in Angstroms	1, -32, 5.280000
9	Cartesian coordinate in z direction, in Angstroms	14, 0.31, -13.41801
10	Mass of atom, in amu (g/mol)	1.008, 12.011, default
11	Partial charge on atom (in e)	0, -0.4231, 2.0
12	Polarizability of atom (in Angstrom^3)	0.922, 4.1801, default
13	Lennard-Jones epsilon (well-depth), in Kelvin [ or Tang-Toennies b parameter ]	32.4, 108.3, default
14	Lennard-Jones sigma (r at zero-energy) in Angstroms [ or Tang-Toennies sigma parameter ]	2.4, 1.99, default
15	Tang-Toennies C6 parameter in ????
16	Tang-Toennies C8 parameter in ????

Example .pdb atoms input file (4 Acetylene molecules):

ATOM      1 C2H2 Ac M    1    -24.395 -25.000 -25.000 12.01070 -0.29121  1.55140  3.00366  3.41104   39.44099 1123.91000
ATOM      2 C2H2 Ac M    1    -25.605 -25.000 -25.000 12.01070 -0.29121  1.55140  3.00366  3.41104   39.44099 1123.91000
ATOM      3 H2C2 Ac M    1    -23.335 -25.000 -25.000  1.00790  0.29121  0.14480  4.65511  1.72667    0.76016  0.00000
ATOM      4 H2C2 Ac M    1    -26.665 -25.000 -25.000  1.00790  0.29121  0.14480  4.65511  1.72667    0.76016  0.00000
ATOM      5 C2H2 Ac M    2    -14.395 -25.000 -25.000 12.01070 -0.29121  1.55140  3.00366  3.41104   39.44099 1123.91000
ATOM      6 C2H2 Ac M    2    -15.605 -25.000 -25.000 12.01070 -0.29121  1.55140  3.00366  3.41104   39.44099 1123.91000
ATOM      7 H2C2 Ac M    2    -13.335 -25.000 -25.000  1.00790  0.29121  0.14480  4.65511  1.72667    0.76016  0.00000
ATOM      8 H2C2 Ac M    2    -16.665 -25.000 -25.000  1.00790  0.29121  0.14480  4.65511  1.72667    0.76016  0.00000
ATOM      9 C2H2 Ac M    3     -4.395 -25.000 -25.000 12.01070 -0.29121  1.55140  3.00366  3.41104   39.44099 1123.91000
ATOM     10 C2H2 Ac M    3     -5.605 -25.000 -25.000 12.01070 -0.29121  1.55140  3.00366  3.41104   39.44099 1123.91000
ATOM     11 H2C2 Ac M    3     -3.335 -25.000 -25.000  1.00790  0.29121  0.14480  4.65511  1.72667    0.76016  0.00000
ATOM     12 H2C2 Ac M    3     -6.665 -25.000 -25.000  1.00790  0.29121  0.14480  4.65511  1.72667    0.76016  0.00000
ATOM     13 C2H2 Ac M    4    -24.395 -15.000 -25.000 12.01070 -0.29121  1.55140  3.00366  3.41104   39.44099 1123.91000
ATOM     14 C2H2 Ac M    4    -25.605 -15.000 -25.000 12.01070 -0.29121  1.55140  3.00366  3.41104   39.44099 1123.91000
ATOM     15 H2C2 Ac M    4    -23.335 -15.000 -25.000  1.00790  0.29121  0.14480  4.65511  1.72667    0.76016  0.00000
ATOM     16 H2C2 Ac M    4    -26.665 -15.000 -25.000  1.00790  0.29121  0.14480  4.65511  1.72667    0.76016  0.00000

Note, the columns that can accept default as input must read in correct element names (from column 3), e.g. Fe, not FE or Fe1, to load the default values. The hardcoded values can be found in the source code. Default values will be loaded automatically for .xyz inputs, but the same naming rule applies.

Default values for mass are taken from the periodic table of elements; For polarizability, from van Duijnen et al. (exponential damping); For Lennard-Jones epsilon, from the Universal Force Field (UFF) (Rappe et al.); For Lennard-Jones sigma, also from UFF.