Basic dynamics

• exclude $\langle$ exclusion policy to use $\rangle$
  Acceptable Values: none, 1-2, 1-3, 1-4, or scaled1-4
  Description:  This parameter specifies which pairs of bonded atoms should be excluded from non-bonded interactions. With the value of none, no bonded pairs of atoms will be excluded. With the value of 1-2, all atom pairs that are directly connected via a linear bond will be excluded. With the value of 1-3, all 1-2 pairs will be excluded along with all pairs of atoms that are bonded to a common third atom (i.e., if atom A is bonded to atom B and atom B is bonded to atom C, then the atom pair A-C would be excluded). With the value of 1-4, all 1-3 pairs will be excluded along with all pairs connected by a set of two bonds (i.e., if atom A is bonded to atom B, and atom B is bonded to atom C, and atom C is bonded to atom D, then the atom pair A-D would be excluded). With the value of scaled1-4, all 1-3 pairs are excluded and all pairs that match the 1-4 criteria are modified. The electrostatic interactions for such pairs are modified by the constant factor defined by 1-4scaling. The van der Waals interactions are modified by using the special 1-4 parameters defined in the parameter files.

• temperature $\langle$ initial temperature (K) $\rangle$
  Acceptable Values: positive decimal
  Description:  Initial temperature value for the system. Using this option will generate a random velocity distribution for the initial velocities for all the atoms such that the system is at the desired temperature. Either the temperature or the velocities/binvelocities option must be defined to determine an initial set of velocities. Both options cannot be used together.

• COMmotion $\langle$ allow center of mass motion? $\rangle$
  Acceptable Values: yes or no
  Default Value: no
  Description: Specifies whether or not motion of the center of mass of the entire system is allowed. If this option is set to no, the initial velocities of the system will be adjusted to remove center of mass motion of the system.

• dielectric $\langle$ dielectric constant for system $\rangle$
  Acceptable Values: decimal $\geq$ 1.0
  Default Value: 1.0
  Description: Dielectric constant for the system. A value of 1.0 implies no modification of the electrostatic interactions. Any larger value will lessen the electrostatic forces acting in the system.

• 1-4scaling $\langle$ scaling factor for 1-4 interactions $\rangle$
  Acceptable Values: 0 $\leq$ decimal $\leq$ 1
  Default Value: 1.0
  Description: Scaling factor for 1-4 interactions. This factor is only used when the exclude parameter is set to scaled1-4. In this case, this factor is used to modify the electrostatic interactions between 1-4 atom pairs. If the exclude parameter is set to anything but scaled1-4, this parameter has no effect regardless of its value.

• seed $\langle$ random number seed $\rangle$
  Acceptable Values: positive integer
  Default Value: pseudo-random value based on current UNIX clock time
  Description: The number used to seed the random number generator if temperature or langevin is selected. This can be used so that consecutive simulations produce the same results. If no value is specified, NAMD will choose a pseudo-random value based on the current UNIX clock time. The random number seed will be output during the simulation startup so that its value is known and can be reused for subsequent simulations. Note that if Langevin dynamics are used in a parallel simulation (i.e., a simulation using more than one processor) even using the same seed will not guarantee reproducible results.

• rigidBonds $\langle$ controls if and how ShakeH is used $\rangle$
  Acceptable Values: none, water, all
  Default Value: none
  Description:  When rigidBonds is all, the bond between each hydrogen and its mother atom is fixed to the nominal bond length given in the parameter file. When water is selected, only the bonds between the hydrogens and the oxygen in water molecules are constrained. For the default case none, no lengths are constrained. Only none can be used with Langevin dynamics.

• rigidTolerance $\langle$ allowable bond-length error for ShakeH (Å) $\rangle$
  Acceptable Values: positive decimal
  Default Value: 0.00001
  Description: The ShakeH algorithm is assumed to have converged when all constrained bonds differ from the nominal bond length by less than this amount.

• rigidIterations $\langle$ maximum ShakeH iterations $\rangle$
  Acceptable Values: positive integer
  Default Value: 100
  Description: The maximum number of iterations ShakeH will perform before giving up on constraining the bond lengths. If the bond lengths do not converge, a warning message is printed, and the atoms are left at the final value achieved by ShakeH. Although the default value is 100, convergence is usually reached after fewer than 10 iterations.