Dynamics

Timestep parameters

• numsteps $<$ number of timesteps $>$
  Acceptable Values: positive integer
  Description: The number of simulation timesteps to be performed. An integer greater than 0 is acceptable. The total amount of simulation time is numsteps$\times$   timestep .

• timestep $<$ timestep size (fs) $>$
  Acceptable Values: non-negative decimal
  Default Value: 1.0
  Description: The timestep size to use when integrating each step of the simulation. The value is specified in femtoseconds.

• firsttimestep $<$ starting timestep value $>$
  Acceptable Values: non-negative integer
  Default Value: 0
  Description: The number of the first timestep. This value is typically used only when a simulation is a continuation of a previous simulation. In this case, rather than having the timestep restart at 0, a specific timestep number can be specified.

Initialization

• temperature $<$ initial temperature (K) $>$
  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 $<$ allow initial center of mass motion? $>$
  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. Note that this does not preclude later center-of-mass motion due to external forces such as random noise in Langevin dynamics, boundary potentials, and harmonic restraints.

• seed $<$ random number seed $>$
  Acceptable Values: positive integer
  Default Value: pseudo-random value based on current UNIX clock time
  Description: 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.

Conserving momentum

• zeroMomentum $<$ remove center of mass drift due to PME $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: If enabled, the net momentum of the simulation and any resultant drift is removed before every full electrostatics step. This correction should conserve energy and have minimal impact on parallel scaling. This feature should only be used for simulations that would conserve momentum except for the slight errors in PME. (Features such as fixed atoms, harmonic restraints, steering forces, and Langevin dynamics do not conserve momentum; use in combination with these features should be considered experimental.) Since the momentum correction is delayed, enabling outputMomenta will show a slight nonzero linear momentum but there should be no center of mass drift.

Multiple timestep parameters

To further reduce the cost of computing full electrostatics, NAMD uses a multiple timestepping integration scheme. In this scheme, the total force acting on each atom is broken into two pieces, a quickly varying local component and a slower long range component. The local force component is defined in terms of a splitting function. The local force component consists of all bonded and van der Waals interactions as well as that portion of electrostatic interactions for pairs that are separated by less than the local interaction distance determined by the splitting function. The long range component consists only of electrostatic interactions outside of the local interaction distance. Since the long range forces are slowly varying, they are not evaluated every timestep. Instead, they are evaluated every $k$ timesteps, specified by the NAMD parameter fullElectFrequency. An impulse of $k$ times the long range force is applied to the system every $k$ timesteps (i.e., the r-RESPA integrator is used). For appropriate values of $k$ , it is believed that the error introduced by this infrequent evaluation is modest compared to the error already incurred by the use of the numerical (Verlet) integrator. Improved methods for incorporating these long range forces are currently being investigated, with the intention of improving accuracy as well as reducing the frequency of long range force evaluations.

In the scheme described above, the van der Waals forces are still truncated at the local interaction distance. Thus, the van der Waals cutoff distance forms a lower limit to the local interaction distance. While this is believed to be sufficient, there are investigations underway to remove this limitation and provide full van der Waals calculations in ${\mathcal O}(N)$ time as well.

One of the areas of current research being studied using NAMD is the exploration of better methods for performing multiple timestep integration. Currently the only available method is the impulse-based Verlet-I or r-RESPA method which is stable for timesteps up to 4 fs for long-range electrostatic forces, 2 fs for short-range nonbonded forces, and 1 fs for bonded forces Setting rigid all (i.e., using SHAKE) increases these timesteps to 6 fs, 2 fs, and 2 fs respectively but eliminates bond motion for hydrogen. The mollified impulse method (MOLLY) reduces the resonance which limits the timesteps and thus increases these timesteps to 6 fs, 2 fs, and 1 fs while retaining all bond motion.

• fullElectFrequency $<$ number of timesteps between full electrostatic evaluations $>$
  Acceptable Values: positive integer factor of stepspercycle
  Default Value: nonbondedFreq
  Description: This parameter specifies the number of timesteps between each full electrostatics evaluation. It is recommended that fullElectFrequency be chosen so that the product of fullElectFrequency and timestep does not exceed $4.0$ unless rigidBonds all or molly on is specified, in which case the upper limit is perhaps doubled.

• nonbondedFreq $<$ timesteps between nonbonded evaluation $>$
  Acceptable Values: positive integer factor of fullElectFrequency
  Default Value: 1
  Description: This parameter specifies how often short-range nonbonded interactions should be calculated. Setting nonbondedFreq between 1 and fullElectFrequency allows triple timestepping where, for example, one could evaluate bonded forces every 1 fs, short-range nonbonded forces every 2 fs, and long-range electrostatics every 4 fs.

• MTSAlgorithm $<$ MTS algorithm to be used $>$
  Acceptable Values: impulse/verletI or constant/naive
  Default Value: impulse
  Description: Specifies the multiple timestep algorithm used to integrate the long and short range forces. impulse/verletI is the same as r-RESPA. constant/naive is the stale force extrapolation method.

• longSplitting $<$ how should long and short range forces be split? $>$
  Acceptable Values: c1, c2
  Default Value: c1
  Description: Specifies the method used to split electrostatic forces between long and short range potentials. The c1 option uses a cubic polynomial splitting function,
  $$S_3(r) = 1 - \frac{3}{2}\left(\frac{r}{r_{\text{cut}}}\right) + \frac{1}{2}\left(\frac{r}{r_{\text{cut}}}\right)^3,$$
  to affect $C^1$ continuity in the splitting of the electrostatic potential [87]. The c2 option uses a quintic polynomial splitting function,
  $$S_5(r) = 1 - 10\left(\frac{r}{r_{\text{cut}}}\right)^3 + 15\left(\frac{r}{r_{\text{cut}}}\right)^4 - 6\left(\frac{r}{r_{\text{cut}}}\right)^5,$$
  to affect $C^2$ continuity in the splitting of the electrostatic potential. The $S_5$ splitting function, contributed by Bruce Berne, Ruhong Zhou, and Joe Morrone, produces demonstrably better long time stability than $S_3$ without requiring any additional computational cost during simulation, since the nonbonded forces are calculated via a lookup table. Note that earlier options xplor and sharp are no longer supported.

• molly $<$ use mollified impulse method (MOLLY)? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: This method eliminates the components of the long range electrostatic forces which contribute to resonance along bonds to hydrogen atoms, allowing a fullElectFrequency of 6 (vs. 4) with a 1 fs timestep without using rigidBonds all. You may use rigidBonds water but using rigidBonds all with MOLLY makes no sense since the degrees of freedom which MOLLY protects from resonance are already frozen.

• mollyTolerance $<$ allowable error for MOLLY $>$
  Acceptable Values: positive decimal
  Default Value: 0.00001
  Description: Convergence criterion for MOLLY algorithm.

• mollyIterations $<$ maximum MOLLY iterations $>$
  Acceptable Values: positive integer
  Default Value: 100
  Description: Maximum number of iterations for MOLLY algorithm.