Dynamics

number of timesteps`numsteps`**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``timestep`.timestep size (fs)`timestep`**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.starting timestep value`firsttimestep`**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.

initial temperature (K)`temperature`**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.allow initial center of mass motion?`COMmotion`**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.random number seed`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.

remove center of mass drift due to PME`zeroMomentum`**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 timesteps,
specified by the NAMD parameter `fullElectFrequency`.
An impulse of times the long range force is applied to the system
every timesteps (i.e., the r-RESPA integrator is used).
For appropriate values of ,
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 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.

number of timesteps between full electrostatic evaluations`fullElectFrequency`**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 unless`rigidBonds all`or`molly on`is specified, in which case the upper limit is perhaps doubled.timesteps between nonbonded evaluation`nonbondedFreq`**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.MTS algorithm to be used`MTSAlgorithm`**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.how should long and short range forces be split?`longSplitting`**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,`c2`option uses a quintic polynomial splitting function,`xplor`and`sharp`are no longer supported.use mollified impulse method (MOLLY)?`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.allowable error for MOLLY`mollyTolerance`**Acceptable Values:**positive decimal**Default Value:**0.00001**Description:**Convergence criterion for MOLLY algorithm.maximum MOLLY iterations`mollyIterations`**Acceptable Values:**positive integer**Default Value:**100**Description:**Maximum number of iterations for MOLLY algorithm.