Main Input Commands

All of these commands would go in the mcmd input file, which would be run by, e.g. ./mcmd myinput.inp

Command	Description	Default
jobname [string]	The job's name.	default_jobname
restart	Automatically restarts a previously halted job by replacing the input atoms file with the existing restart.pdb, and saving directory files to saved_dataX where X automatically counts from 1. YOU MUST USE THE input_atoms command if you plan to restart a job.	off
mode [mc | md | sp | opt]	mc for Monte Carlo; md for Molecular Dynamics. sp for classical single-point energy and multipoles. opt for classical optimization.	NONE
omp [int]	Enables OpenMP parallelization for faster simulation. Argument is number of threads. 0 will disable OpenMP. Requires compilation with OpenMP enabled.	0
checkpoints_option [on | off]	Displays checkpoints from code with relevant timing info (for debugging).	off
ensemble [nve|nvt|npt|uvt]	Thermodynamic ensemble. nve = Microcanonical; nvt = Canonical; npt = Isobaric,Isothermal (Gibbs); uvt = Grand Canonical.	NONE
input_atoms [string]	Takes the filename of input atoms in .pdb form (see examples). Not required for uVT simulation.	NONE
input_atoms_xyz [string]	Option to use an XYZ file for input atoms. The string is the filename. This assumes all atoms are Frozen (e.g. part of a MOF) and uses periodic-table mass, UFF LJ params, and van Duijnen polarizabilities by default. Point-charges (in e) are optional and can be placed in the 5th column.	NONE
output_traj_xyz [string]	Takes the filename in which to write .xyz trajectory file every corrtime. Especially useful if you view trajectories for uVT simulation using VMD.	traj.xyz.
output_traj_pdb [string]	Takes the filename in which to write .pdb trajectory file every corrtime.	traj.pdb.
draw_box_option [on|off]	Enables creation of the simulation box in the restart_pdb and output_traj_pdb files.	on
restart_pdb [string]	Filename for the restart input_atoms file generated at each corrtime.	restart.pdb.
thermo_output [string]	Takes the filename in which to write thermodynamic data at each corrtime: energy, temperature, pressure, etc.	thermo.dat
potential_form [lj | ljes | ljespolar | ljpolar | tt | ttes | ttespolar | commy | commyes | commyespolar]	Dictates which functions to use for potential energy and force (MD only) calculations: lj=Lennard-Jones repulsion-dispersion; tt=Tang-Toennies RD; es=Ewald electrostatics; polar=polarization energy; commy=a VDW RD potential which is a hybrid of LJ and a form from a 1961 paper linked in commy.cpp.	lj
rd_lrc [on|off]	Enables Lennard-Jones long-range corrections to the potential energy.	on
ewald_es [on|off]	Enables Ewald-method calculation of electrostatic energy (including long-range).	on
ewald_kmax [int]	Specifies the maximum k-space vector for Ewald energy/force computation. >3 is generally good. Can be very expensive for large systems if >=5.	7
polar_max_iter [int]	Change the max number of iterations for dipole solver in polarization energy calculation.	4
dipole_precision [double]	Turns dipole-convergence-by-dipole-precision on (instead of fixed maximum iterations). Expressed in Debye. (the iteration-cap is the default method). A good value is between 10e-7 and 10e-4.	NONE
full_A_matrix [on|off]	Option to enable the full Thole Polarization A matrix -- takes more (~double) memory but runs faster.	on
pdb_traj_option [on|off]	Enables PDB trajectory output in output_traj_pdb filename.	off
xyz_traj_option [on|off]	Option to (also) write .xyz trajectory output.	on
big_pdb_traj [on|off]	Forces frozen atoms to be (re-)written in trajectory steps in PDB.	off
big_xyz_traj [on|off]	Forces frozen atoms to be (re-)written in trajectory steps in XYZ.	off
com_option [on|off]	Enables on-the-fly center-of-mass calculation which adds a COM atom to the output files in each frame.	off
pdb_long [on|off]	Enables long (%8.6f instead of %8.3f) output for greater precision on atom coordinates. Do NOT enable if you plan to view .pdb output in VMD.	off
dist_within [on|off]	Enables on-the-fly counter of atoms within a specified radius from the origin at each corrtime.	off
dist_within_target [string]	Takes the (PDB input label) name of the atom to calculate for dist_within.	NONE
dist_within_radius [double]	Takes the radius from the origin in which to count occurrences of selected atom.	NONE
auto_center [on|off]	Enables automatic centering of all atoms to the origin (0,0,0) before beginning simulation. Important to make sure atoms fit in periodic box.	on
temperature [double]	Temperature in K for fixed-T simulations.	NONE
pressure [double]	Pressure in atm for fixed-P simulations (including uVT because chemical potential is auto-generated from pressure using equations-of-state).	1.0
sig_override [string] [double]	Manually changes the LJ sigma parameter for atoms by name. For multiple, issue this command in multiple lines. (Units = Angstrom)	NONE
eps_override [string] [double]	Does likewise for LJ epsilon parameter. (Units = Kelvin)	NONE
charge_override [string] [double]	Does likewise for the partial charge of this site. (Units = elementary charge)	NONE
radial_dist [on|off]	Enables radial-distribution calculation, which updates every corrtime.	off
radial_bin_size [double]	Specifies the bin size for g(r) in A.	0.1
radial_max_dist [double]	Sets the cutoff for relevant g(r) distance calculations between atoms.	10.0
radial_centroid [string]	Supplies name of atom (site) to calculate as the the center of g(r) interactions.	NONE
radial_counterpart [string]	Supplies the other atom to calculate distance from radial_centroid.	NONE
radial_file [string]	Specifies name of output file for g(r). Supplies bin-counts as a function of pair-distance.	radial_distribution.datX (X = pair id for multiple)
radial_exclude_molecules [on|off]	Option to exclude intramolecular distances in g(r) pair calculations.	off
histogram [on|off]	Option for histogram output (which can be viewed in VMD).	off
histogram_output [string]	Filename for histogram output.	histogram.dx
histogram_resolution [double]	Resolution of histogram bins in Angstroms.	0.7
lj_uff [on|off]	Option to set all atoms' Lennard-Jones sigma and epsilon to UFF (Rappe et al.) values (overrides other input)	off
vand_polar [on|off]	Option to set all atoms' point-polarizability parameters to van Duijnen values (overrides other input)	off
manual_cutoff [double]	Overrides the pair-interaction spherical cutoff radius (auto-calculated from box parameters as 1/2 min. length) with user-defined value.	NONE
crystalbuild [on|off]	Enables the crystal builder (to build super-cells automatically).	off
crystalbuild_x [int]	Multiplicity of crystal in x-direction (e.g. 2 will duplicate the cell in x).	1
crystalbuild_y [int]	Same for y-direction.	1
crystalbuild_z [int]	Same for z-direction.	1
crystalbuild_includemovers [on|off]	Option to include movable molecules when duplicating system.	off
makefrags [int]	Enables the fragment-maker and creates the number of fragments specified. The function loops through unique atoms by their name (in the .pdb input) and makes fragments that bury each atom in a fractal-like pattern.	NONE
atoms_per_frag [int, int, int,..]	Sets the number of atoms that will be created within each fragment. You can do multiple #'s for different fragment sizes.	250
frag_bondlength [double]	Sets the initial/default bond-length (in Angstroms) for the fragment-maker. If a fragment fails to build within this constraint, it will grow the bond-length until the goal number of atoms is obtained.	2.1
scale_charges [double]	Multiplies all frozen-atom charge parameters by this factor before running the simulation.	NONE
sorbate_name [string] [string] [string...]	Allows user-selected sorbate models (you need not include the sorbate [or anything at all] in the input_atoms file IF this is used). You MUST include sorbate_fugacities if multi-sorbate (this command) is used in the uVT ensemble.	NONE
sorbate_fugacities [double] [double] [double...]	Partial pressures (in atm, as explicit fugacities) of sorbates, e.g. 10 10 would yield a total pressure of 20 atm.	NONE
no_zero_option [on|off]	Option to disallow zero movable molecules in the simulation system.	off
write_lammps [on|off]	Writes LAMMPS-style inputs from MCMD input at simulation start (for MD simulations).	off
bias_uptake [double] [N | wt% | wt%ME | mmol/g | mg/g | cm^3/g | g/mL | g/cm^3]	Sets a "goal-uptake", which is achieved in uVT single-sorbate-only simulations by biasing insertions and preventing removes until the goal N is reached. Can accelerate equilibration/loading significantly especially if a good reference value is known. After this, the system equilibrates normally.	NONE

Monte Carlo

Command	Description	Default
mc_corrtime [int]	The MC step interval at which output is generated, observable averages re-calculated, etc.	1000
finalstep [int]	Specifies the last step to perturb system and calculate energy in MC.	NONE
rotate_option [on|off]	Enables rigid-body molecular rotations for movable molecules in MC.	on
volume_change [double]	A factor that is used to change the volume in NPT MC simulations.	2.5 -- Frenkel's value.
vcp_factor [double]	A factor used to calculate the probability of doing a volume change in NPT.	1.0 -- Frenkel's value.
displace_factor [double]	A factor (length in Angstroms) used to calculate random translations of molecules in MC simulations.	1.0
insert_factor [double]	The probability of doing an insert/delete move in uVT MC simluations.	0.5
rotate_angle_factor [double]	A factor used to calculate a random angle of rotation for displacement in MC simluations.	360.0
mc_pbc [on|off]	Enables periodic-boundary conditions.	on
total_energy [double]	Potential energy in K as fixed value for NVE simulations. (Should usually be negative!).	NONE
simulated_annealing [on|off]	Option for simulated annealing.	off
simulated_annealing_schedule [double]	A factor for exponentially decreasing temperature in S.A.	0.9999
simulated_annealing_target [double]	Target end-temperature (in Kelvin) for simulated annealing.	0.0
fugacity_single [h2|co2|n2|ch4]	in uVT, specifies the molecule to calculate fugacity (from input pressure) at startup.	NONE
step_offset [int]	An offset value for Monte Carlo steps, e.g. to pickup restarts and count where you left off.	0
auto_reject_option [on|off]	Enables auto-reject feature which can speed up Monte Carlo, forced off for Molecular Dynamics. Only useful when using at least the LJ potential.	on
auto_reject_r [double]	Parameter in Angstroms to auto-reject moves if a pair distance is less than this value.	0.76
feynman_hibbs [on|off]	Enables Feynmann-Hibbs Quantum corrections to energy calculation (useful especially for small molecules e.g. hydrogen).	off
fh_order [2|4]	Chooses second or fourth order correction for Feynman-Hibbs corrections.	4

Molecular Dynamics

Command	Description	Default
integrator [rk4|vv]	The method for integrating Newton's equations of motion. rk4 = Runge Kutte 4th order; vv = Velocity verlet.	vv
md_corrtime [int]	The step interval at which output is generated, averages re-calculated, etc.	50
md_pbc [on|off]	Enables periodic-boundary conditions.	on
md_init_vel [double]	User defined initial velocities for movable molecules. Will randomize directions based on this magnitude in A/fs. If this is not supplied, initial velocities will be determined from temperature.	NONE
md_dt [double]	The actual time step used for Molecular Dynamics, in fs.	0.1
md_ft [double] [string]	The time to stop the simulation. Units can be fs, ps, ns, us, or ms.	10000 fs
md_mode [rigid|atomic|flexible]	MD mode. rigid keeps molecules rigid, intact, and allows them to rotate. atomic treats all atoms as free-moving regardless of assignment in input_atoms file. flexible enables bonding parameters for movable molecules.	molecular
md_rotations [on|off]	Enables molecular rotations in MD.	on
md_translations [on|off]	Enables molecular translations in MD. Turning this off is useful, for example, with molecular crystal simulation.	on
cuda [on|off]	Enables GPU-accelerated Molecular Dynamics (by calculating forces on GPU). Only compatible with CUDA GPUs.	off
cuda_block_size [int]	Specifies threads-per-block for CUDA parallel computation. Good values are typically multiples of the common warp size, 32.	256
md_insert_frequency [int]	Interval number of steps at which to attempt an insert/delete in uVT MD.	20
calc_pressure_option [on\off]	Enables virial pressure calculator (NVT ensemble only).	on for NVT; off for others.
external_force [double] [double] [double] [int]	Applies a constant external force to all movable molecules. Expressed as a vector (x,y,z) in nanoNewtons nN followed by an integer of how often (in steps) the force should apply. 1.0 0 0 1 is a moderate force in the +x direction for molecules applied every step.	0.0 0.0 0.0 1
sorbate_dofs [int,int,...]	Manually enter the number of degrees of freedom for each prototype movable molecule.	NONE
kspace_option [on|off]	Enables computation of Ewald k-space (long-range) forces in MD.	on
input_structure_ff [on|off]	Option to use the input atomic structure for equilibrium bondlength, angle and dihedral parameters. If off, MCMD defaults to UFF/UFF4MOF parameters.	off
thermostat [andersen|nose-hoover]	Chooses a thermostat for NVT MD simulation. nose-hoover cannot be used for uVT MD simulation.	nose-hoover
nh_q [double]	Manually set the Nose-Hoover Q parameter in K fs^2.	none
nh_q_scale [double]	Scale the Nose-Hoover Q parameter by this factor. Recommended values 0.8 - 2.0.	1.0

Optimizations

Command	Description	Default
opt_mode [mc|sd]	Optimization method: mc = Monte Carlo; sd = Steepest Descent.	sd
bondlength [double]	Assigns maximum distance, in Angstroms, to dynamically define bonds.	1.5
opt_convergence [double]	Assigns the convergence delta-energy, in kcal/mol.	0.00001
opt_step_limit [int]	Assigns maximum number of optimization steps for convergence.	10000
opt_bonds [on|off]	Includes bonded stretching for optimization/flexible MD calculation.	on
opt_angles [on|off]	Includes angle bending for optimization/flexible MD calculation.	on
opt_dihedrals [on|off]	Includes dihedral bending (torsions) for optimization/flexible MD calculation.	on
opt_LJ [on|off]	Includes non-bonded Lennard-Jones interactions for optimization/flexible MD calculation.	on
opt_ES [on|off]	Includes non-bonded electrostatic interactions for optimization/flexible MD calculation.	on

Single Point Calculations

Command	Description	Default