Molecular Dynamics

• Time_step <value>

  Time step in femtoseconds. This is the long time step in case of the double time step algorithm.

  Default: 2 fs.

• Number_steps <number>

  How many MD steps to run.

• Double_timestep <number>

  Double time step algorithm by Tuckerman et al. <number> is the number of short time steps in one long. The keyword cannot be used simultaneously with Constrain.

• Constrain <toler> <i_1> <i_2> <i_3> .... <i_ntypes>

  Use SHAKE algorithm to constrain the bond lengths. The option cannot be used with Double_timestep. <toler> is the tolerance level.

  <i_1> <i_2> ... <i_ntypes> are numbers 0 or 1, which specify whether (1) or not (0) to apply constraints to molecules of each species.

• R_cutoff <value>

  Cut-off (in Å) for the Lennard-Jones and real-space part of the electrostatic forces.

  Default: 12 Å

• R_short <value>

  Cut-off (in Å) for Lennard-Jones forces computed each short-time step (has an effect only in double-time step algorithm)

  Default: 5 Å

• Neighbour_list <number>

  Update the list of neighbors (Verlet list) every <number> steps

  Default: 10

• Electrostatics <type> [<A> <B>]

  How to treat electrostatics

  <type> may be Ewald (default), RF (reaction field) and Cutoff

  For Ewald: A is $\alpha /R_{cutoff}$, where $\alpha$ is the Ewald convergence parameter. Precision of the real-space Ewald part is determined by $erfc(A)$. $B$ defines the number of terms in the reciprocal part. It cuts the reciprocal series when expression in the exp of the reciprocal part exceeds $B$. Recommended values A = 2.5 - 3; B = 7 - 10.

  For reaction field, A is the dielectric permittivity and B is the Debye screening length in Å. Setting the Debye length to 0 means an infinite Debye length, i.e non-conducting solution.

  If <type> is ``Cutoff'', parameters $A$ and $B$ are not necessary, and no special treatment of electrostatic forces out of $R_{cutoff}$ takes place.

  Default: Ewald method with A=2.8 and B=9.

• Cut_forces <value>

  If this option is specified and the absolute force acting on any atom exceeds the specified <value>, the force will be cut to this level while maintaining the direction. The value is given in Å and has a sense of the maximum allowed additional displacement during one time step ( F*dt**2/m ) caused by this force

  Default: Do not cut forces

• Combination_rule <type>

  Use another (than Lorentz-Berthelot) combination rule for Lennard-Jones parameters for different types

  type may be one of the following:

  Sigma_geom - LJ $\sigma$ parameter is calculated as a geometrical average of the both types (as for example in the OPLS force field)

  Kong - use Kong rules (J.Kong, J.Chem.Phys., 59, 2464, (1973))

  Default: use Lorentz-Berthelot combination rules

• Bind_atoms <file> <deviation>

  If this keyword is specified, atoms defined in file <file> will be bound to corresponding positions (given in the same file) by a harmonic potential with characteristic deviation given by <deviation>