CYANA Command: md - Revision history

Masayo: /* Parameters */

2009-08-12T13:29:24Z

Parameters

← Older revision		Revision as of 15:29, 12 August 2009
Line 2:		Line 2:
	== Parameters ==		== Parameters ==

	; steps=''integer'' (required)		; steps=''integer'': (required)
	; dt=''real'': (default: 0.05)		; dt=''real'': (default: 0.05)
	; level=''integer'': (default: 0)		; level=''integer'': (default: 0)
Line 14:		Line 14:
	; vdwupdate=''integer'': (default: 100)		; vdwupdate=''integer'': (default: 100)
	; exact		; exact
	; continue		; continue

	== Description ==		== Description ==

Masayo: /* Description */

2009-08-07T08:19:44Z

Description

← Older revision		Revision as of 10:19, 7 August 2009
Line 18:		Line 18:
	== Description ==		== Description ==

	~~This command performs~~ molecular dynamics simulation in torsion angle		Performs molecular dynamics simulation in torsion angle space (torsion angle dynamics) with the following parameters:
	space (torsion angle dynamics) with the following parameters:		:; '''steps''' : Number of time steps.
			:; '''dt''' : Time step length.
	steps ~~number~~ of time steps		:; '''level''' : Maximal residue index difference for restraints that are included into the target function.
	dt ~~time~~ step length		:; '''temperature''' : Temperature of the heat bath to which the system is coupled, or 0.0 for a simulation at constant total energy.
	level ~~maximal~~ residue index difference for restraints		:; '''accuracy''' : Desired relative accuracy of energy conservation for automatic time step length adaption, or 0.0 for a simulation with constant time step length.
	that are included into the target function		:; '''tau''' : Coupling constant for temperature and time step length updates, given in units of the time step length.
	~~temperature~~ temperature of the heat bath to which the system		:; '''nprint''' : Number of time steps between intermediate output.
	is coupled, or 0.0 for a simulation at constant		:; '''tinit''' : Initial time.
	total energy		:; '''estart''' : Initial temperature (kinetic energy per degree of freedom).
	accuracy ~~desired~~ relative accuracy of energy conservation		:; '''angdev''' : Maximal change of a torsion angle (in degrees) between two updates of the van der Waals pair list.
	for automatic time step length adaption, or 0.0		:; '''vdwupdate''' : Maximal number of torsion angle dynamics steps between two updates of the van der Waals pair list.
	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		The '''md''' command can start a new torsion angle dynamics run, or, if the
Line 52:		Line 40:
	end of the previous '''md''' command are used and all parameters that		end of the previous '''md''' command are used and all parameters that
	are not specified explicitly are kept at the values of the previous		are not specified explicitly are kept at the values of the previous
	'''md''' command. The parameters '''tinit''' and '''estart''' are not allowed in		'''md''' command. The parameters ''tinit''' and ''estart''' are not allowed in
	conjunction with the '''continue''' option.		conjunction with the '''continue''' option.

	If the parameter '''temperature''' is set to 0.0, a molecular dynamics		If the parameter ''temperature'' is set to 0.0, a molecular dynamics
	simulation at constant energy is performed. Normally, however, the		simulation at constant energy is performed. Normally, however, the
	system is weakly coupled to a heat bath of the given ''temperature'' with		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.,		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		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		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.,		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,~~		''s''(''n'') = (''n'' - 1)/(''N'' - 1) for step ''n'' out of a total of ''N'' = ''steps'' time steps.
	~~where N denotes the value of the parameter~~ '''steps'''.

	If the ''accuracy'' reference value for the accuracy of energy		If the ''accuracy'' reference value for the accuracy of energy
Line 73:		Line 60:
	control. The time step length corresponds to the torsional velocities,		control. The time step length corresponds to the torsional velocities,
	and the relative change of the total (kinetic plus potential) energy		and the relative change of the total (kinetic plus potential) energy
	corresponds to the temperature. In this case, the parameter ~~'''~~dt~~'''~~		corresponds to the temperature. In this case, the parameter "dt"
	specifies the only initial value for the time step length.		specifies the only initial value for the time step length.

Line 105:		Line 92:
	1000 76.882 1654.211 5322.900 6977.111 2.779 15.591 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		Intermediate output is written only if the parameter ''nprint'' has a
	positive value. All energies are measured in target function units.		positive value. All energies are measured in target function units.
	Temperatures are measured in target function units per degree of		Temperatures are measured in target function units per degree of

Admin: 1 revision

2009-01-29T11:26:55Z

1 revision

New page

== 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]]