Temperature and pressure coupling

MD workshops
26-10-2004
Why control the temperature and pressure?

isothermal and isobaric simulations (NPT) are most

relevant to experimental data

constant NPT ensemble: constant number of particles,

pressure, and temperature
 Causes of temperature and pressure
fluctuations
the temperature and pressure of a system tends to drift due
to several factors:

drift as a result of integration errors

drift during equilibration
heating due to frictional forces
heating due to external forces
 Temperature coupling methods in
GROMACS
weak coupling
exponential relaxation Berendsen temperature
coupling (Berendsen, 1984)

extended system coupling

oscillatory relaxation Nos-Hoover temperature
coupling (Nos, 1984; Hoover, 1985)
 Berendsen temperature coupling

there is weak coupling to an external heat bath

deviation of system from a reference temperature To is
corrected

exponential decay of temperature deviation

 the temperature of a system is related to its kinetic
energy, therefore, the temperature can be easily altered
by scaling the velocities vi by a factor

is the temperature coupling time constant

need to specify in input file (*.mdp file)
 Some notes on Berendsen weak coupling
algorithm
very efficient for relaxing a system to the target
temperature
prolonged temperature differences of the separate
components leads to a phenomenon called hot-
solvent, cold-solute, even though the overall
temperature is at the correct value

Solutions:
1. apply temperature coupling separately to the solute
and to the solvent problem with unequal
distribution of energy between the different
components
solutions continued

2. stochastic collisions (Anderson, 1980)

- a random particles velocity is reassigned by random
selection from the Maxwell-Boltzmann distribution at
set intervals does not generate a smooth
trajectory, less realistic dynamics
3. extended system (Nos, 1984; Hoover 1985)
- the thermal reservoir is considered an integral part of
the system and it is represented by an additional
degree of freedom s
- used in GROMACS
 Nos-Hoover extended system

canonical ensemble (NVT)

more gentle than Anderson where particles suddenly

gain new random velocities

the Hamiltonian is extended by including a thermal

reservoir term s and a friction parameter , in the
equations of motion
H = K + V + Ks + Vs
 Nos-Hoover extended system

The particles equation of motion:

is a dynamic quantity with its own equation of motion:

is proportional to the temperature coupling time

constant (specified in *.mdp file)
 the strength of coupling between the reservoir and the
system is determined by
- when is too high slow energy flow between
system and reservoir
- when is too low rapid temperature
fluctuations
 Nos-Hoover produces an oscillatory relaxation, it takes
several times longer to relax with Nos-Hoover coupling
than with weak coupling

can use Berendsen weak coupling for equilibration to

reach desired target, then switch to Nos-Hoover

Nos-Hoover chain: the Nose-Hoover thermostat is

coupled to another thermostat or a chain of thermostats
and each are allowed to fluctuate
 Pressure coupling

The system can be coupled to a pressure bath as in

temperature coupling

weak coupling:
exponential relaxation Berendsen pressure coupling

extended ensemble coupling:

oscillatory relaxation Parrinello-Rahman pressure
coupling (Parrinello and Rahman, 1980, 1981, 1982)
 Berendsen pressure coupling

equations of motion are modified with a

first order relaxation of P towards a reference Po

rescaling the edges and the atomic coordinates ri at

each step by a factor u leads to volume change
u is proportional to which is the isothermal
compressibility of the system and which is the pressure
coupling time constant. Both values must be specified in
*.mdp file
 Berendsen scaling can be done:
1. isotropically scaling factor is equal for all three
directions i.e. in water
2. semi-isotropically where the x/y directions are
scaled independently from the z direction i.e. lipid
bilayer
3. anisotropically scaling factor is calculated
independently for each of the three axes
 Parrinello-Rahman pressure coupling

volume and shape are allowed to fluctuate

extra degree of freedom added, similar to Nos-Hoover
temperature coupling, the Hamiltonian is extended

box vectors and W-1

are functions of M

W-1 determines the strength of coupling

have to provide and
in the input file (*.mdp file)
 if your system is far from equilibrium, it may be best to
use weak coupling (Berendsen) to reach target pressure
and then switch to Parrinello-Rahman as in temperature
coupling
in most cases the Parrinello-Rahman barostat is
combined with the Nos-Hoover thermostat
the extended methods are more difficult to program but
safer
 Weak coupling in *.mdp file

; OPTIONS FOR WEAK COUPLING ALGORITHMS =

; Temperature coupling =
tcoupl = berendsen
; Groups to couple separately =
tc-grps = Protein SOL_Na
; Time constant (ps) and reference temperature (K) =
tau-t = 0.1 0.1
ref-t = 300 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau-p = 1.0
compressibility = 4.5E-5
ref-p = 1.0
 Extended system coupling in *.mdp file

; OPTIONS FOR WEAK COUPLING ALGORITHMS =

; Temperature coupling =
tcoupl = nose-hoover
; Groups to couple separately =
tc-grps = PROTEIN SOL_Na
; Time constant (ps) and reference temperature (K) =
tau-t = 0.5 0.5
ref-t = 300 300
; Pressure coupling =
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau-p = 5.0
compressibility = 4.5E-5
ref-p = 1.0
 References
Berendsen, H.J.C., Postma, J.P.M., DiNola, A., Haak, J.R. Molecular
dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690,
1984
Nos, S. A molecular dynamics method for simulations in the canonical
ensemble. Mol. Phys. 52:255-268, 1984
Hoover, W.G. Canonical dynamics: equilibrium phase-space distributions.
Phys. Rev. A 31:1695-1697, 1985
Berendsen, H.J.C. Transport properties computed by linear response
through weak coupling to a bath. In: Computer Simulations in Material
Science. Meyer, M., Pontikis, V. eds. Kluwer 1991, 139-155
Parrinello, M., Rahman, A. Polymorphic transitions in single crystals: A new
molecular dynamics method. J. Appl. Phys. 52:7182-7190, 1981
Nos, S., Klein, M.L. Constant pressure molecular dynamics for molecular
systems. Mol. Phys. 50: 1055-1076, 1983