Input File keywords

• temperature [Kelvin]:
  Specify the temperature of the system
  
  
• timestep [Smallest Timestep (ps)] [Largest Timestep (ps)] [Radial scale start (Angstroms)] [Radial scale end (Angstroms)]:
  Specify the linearly scaling timestep. The first two values specificy the minimum and maximum timestep values, while the last two values specify the radial distances from which the timestep is scaled from the minimum to the maximum value.
  
  
• order [integer]:
  Specify the order of finite difference force approximation for potential grids. (Default=2)
  
  
• threads [# of threads]:
  Specify the number of the parallel threads (Cilk workers) to use
  
  
• writeTraj [# of steps]:
  Specify the frequency of trajectory writes in number of steps per write.
  
  
• writeLog [# of steps]:
  Specify the frequency of reporting rate constant data to log file
  
  
• writeRestart [# of steps]
  Specify the frequency of writing restart files in number of steps per write
  
  
• logBinders:
  If this keyword appears in the input file, individual binding events will be logged.
  
  
• logExiters:
  If this keyword appears in the input file, unsuccessful simulation replicates that leave the simulation space will be logged.
  
  
• convergence [Convergence criteria]:
  Specify the criteria with which the convergence of the Beta value (bound ligand fraction) is determined. The convergence test is based on the standard error of the Beta value. As an example, a convergence value of 0.0001 will ensure that the standard error of Beta is <= 0.0001.
  
  
• convWindow [# of completed simulations]:
  Specify the number of the most recent completed replicate simulations to consider when calculating the standard error for the convergence test.
  
  
• useRestart [yes/no]:
  Read ligand starting positions, trajectory lifetimes, and binding information from restart files if "yes".
  
  

• fixedReceptor [yes/no]:
  Set to "yes" if receptor is stationary in the conditions being simulated. Will use self- or relative diffusion coefficient in Langevin equation of motion for "yes" or "no", respectively .
  
  

• receptor [PQR filename]:
  Specify the receptor system for the simulation. This file is used to determine the center of the simulation space. Actual representations of the receptor system must be specified by grid files.
  
  

• grid [Grid Type] [BPM/BXM grid filename]:
  Specify a grid-based representation of a receptor.
  Grid Type can be:
       ex for an exclusion grid (BXM)
       es for an electrostatic potential grid (BPM)
       d for a ligand desolvation potential grid (BPM)
       a ligand atom type as it appears in the ligand PQR file (ex: C, O, H, N, etc.) for a Lennard-Jones potential grid (BPM).
  
  

• ligand [PQR filename]:
  Specifies the structure file for a ligand to be diffused in the current simulation session definition. This can be a single structure or multiple ligand conformations separated by "END" text.
  
  

• bindgroups [X] [Y] [Z] [radius (Angstroms)] [lig atom ID]:
  Specifies the binding site cartesian coordinate, binding distance threshold, and ligand atom ID for any number of binding criteria.
  Individual criteria are separated by the text "OR". To force two or more criteria to be met simultaneously, omit "OR". See example input file.
  
  
• ligandStart Specifies ligand starting conditions. There are five acceptable formats of this keyword:
  (1) [X Y Z] If three numbers are given, they will be interpreted as the Cartesian X Y Z coordinates for a single-point ligand start.
  (2) [b q] If two numbers are given, they will be interpreted as the radii of b and q spheres respectively for a NAM configuration simulation. Use this to perform a NAM simulation.
  (3) [height (Angstroms)] If one number is given, it will be interpreted as the height above the receptor for a ligand starting plane.
  (4) [string] The text "random" will start ligands from randomly-chosen positions within the simulation space.
  (5) [X Y Z cutoff (Angstroms)] Entering four numbers will initiate a substrate transfer simulation divided into direct and indirect transfer portions. The first three numbers will be interpreted as the X Y Z coordinates for a single-point ligand start (the direct part), and the fourth number is both the b sphere of a NAM simulation (the indirect part) and exit radius of the direct part of the simulation. See this reference for more information.
  
  
• boundary [string] Enables cuboid, hexagonal prismatic, or spherical simulation cell shapes. These are specified with text strings "rect", "hex", or "sphere", respectively.
  
  
• boundWall [distance (Angstroms)] Controls placement of cell edges in X and Y dimensions. For a cuboid, this is half the side length in X and Y. For a hexagonal prism, this is the apothem of the hexagonal faces. For a sphere, this is the radius.
  
  
• ceiling [distance (Angstroms)] In simulations of a surface-bound receptor, this can be used to place a "hard" wall at the top of the simulation cell. This is the distance above the bottom-most part of the receptor at which the ceiling will be placed.
  
  

Example input files:

Example 1: Default session, planar ligand start, cuboid periodic cell, hard ceiling, three binding criteria (final criterion requires two conditions be met simultaneously)

Example 2: NAM simulation, b=100, q=300, single binding criterion