CYANA Command: md

Parameters

steps=integer (required)

dt=real

(default: 0.05)

level=integer

(default: 0)

temperature=string

(default: 0.1)

accuracy=string

(default: 0.0)

tau=real

(default: 0.0)

nprint=integer

(default: 0)

tinit=real

(default: 0.0)

estart=real

(default: 0.01)

angdev=real

(default: 10.0)

vdwupdate=integer

(default: 100)

exact

continue

Description

This command performs molecular dynamics simulation in torsion angle space (torsion angle dynamics) with the following parameters:

 steps        number of time steps
 dt           time step length
 level        maximal residue index difference for restraints
              that are included into the target function
 temperature  temperature of the heat bath to which the system
              is coupled, or 0.0 for a simulation at constant
              total energy
 accuracy     desired relative accuracy of energy conservation
              for automatic time step length adaption, or 0.0
              for a simulation with constant time step length
 tau          coupling constant for temperature and time step
              length updates, given in units of the time step
              length
 nprint       bumber of time steps between intermediate output
 tinit        initial time
 estart       initial temperature (kinetic energy per degree
              of freedom)
 angdev       maximal change of a dihedral angle (in degrees)
              between two updates of the van der Waals pair list
 vdwupdate    maximal number of TAD steps between two updates
              of the van der Waals pair list

The md command can start a new torsion angle dynamics run, or, if the option continue is set, continue a preceding torsion angle dynamics calculation. A new molecular dynamics trajectory starts at time tinit (normally 0.0) with random torsional velocities, chosen as Gaussian random variables such that the initial temperature (kinetic energy per degree of freedom) equals estart. If the md command is used to continue a previous calculation, then the velocities from the end of the previous md command are used and all parameters that are not specified explicitly are kept at the values of the previous md command. The parameters tinit and estart are not allowed in conjunction with the continue option.

If the parameter temperature is set to 0.0, a molecular dynamics simulation at constant energy is performed. Normally, however, the system is weakly coupled to a heat bath of the given temperature with a time constant of tau times the time step length (Berendsen et al., 1984). The temperature can either be a constant or a function of the parameter s, which varies linearly from 0 to 1 during the time steps that are performed during the execution of the md command, i.e., s(n) = (n - 1)/(N - 1) for step n out of a total of N time steps, where N denotes the value of the parameter steps.

If the accuracy reference value for the accuracy of energy conservation has a positive value, then the length of the integration time step will be adapted during the molecular dynamics simulation such that the relative change of the total energy in successive integration steps is close to the given accuracy. The adaption of the time step length works in the same way as the temperature control. The time step length corresponds to the torsional velocities, and the relative change of the total (kinetic plus potential) energy corresponds to the temperature. In this case, the parameter dt specifies the only initial value for the time step length.

The van der Waals interaction pair list is updated after at most vdwupdate torsion angle dynamics steps or whenever a torsion angle has changed its value by more than angdev degrees since the last update of the an der Waals interaction list.

The "leap-frog" algorithm is used to perform the torsion angle dynamics steps. Usually, torsional accelerations are computed on the basis torsional velocity values that are linearly extrapolated from those half a time-step earlier. More exact torsional acceleration values that are calculated iteratively (Mathiowetz et al., 1994) will be used if the option exact is set.

One line of output is written every nprint time steps, giving the current step, current time, potential energy (target function value), kinetic energy, total energy, the root-mean-square torsion angle change per time step (in degrees; averaged over all time steps since the last output), the maximal torsion angle change per time step (in degrees; since the last output), the number of updates of the van der Waals interaction list since the last output, and the number of target function evaluations since the last output. For example:

 step     time      Epot      Ekin      Etot  rmsdev  maxdev  #up    #f
    0    0.000 17817.672  5776.000 23593.672                    1     1
  200   13.778  4367.090  7321.274 11688.363   2.842  18.576    4   204
  400   28.471  2896.928  6002.219  8899.147   2.763  16.301    4   206
  600   42.374  2464.380  6988.264  9452.645   2.330  13.941    4   200
  800   60.234  2496.055  6167.296  8663.351   2.815  15.211    4   200
 1000   76.882  1654.211  5322.900  6977.111   2.779  15.591    4   200

Intermediate output is written only if the parameter nprint has a positive value. All energies are measured in target function units. Temperatures are measured in target function units per degree of freedom. Each rotatable torsion angle constitutes a degree of freedom.

A warning is printed if in a single time step the value of a dihedral angle changed by more than 35, and an error occurs if the change exceeds 90 degrees.

Further reading:

• Guntert et al. J. Mol. Biol. 278, 353-378 (1997).
• Jain et al. J. Comput. Phys. 106, 258-268 (1993).
• Matthiowetz et al. Proteins 20, 227-247 (1994).
• Berendsen et al. J. Chem. Phys. 81, 3684-3690 (1984).

See also

• anneal
• calc_all