Pressure Control in NPT

MD Simulations
The pressure, P, can be calculated using Clausius virial theorem
as

1  
N −1 N
PV = Nk BT −
3
 rij  fij
i =1 j i
with the box volume V
and Virial tensor as
second term

2 1 N
T= K . E. K . E. =  mi vi2
3 Nk B 2 i
 Berendsen barostat
H.J.C. Berendsen et al., J. Chem. Phys. 81, 3684 (1984)

• In the Berendsen method, the system is weakly coupled to an

external bath.

• Similar to the temperature coupling, an extra term is added to

the equations of motion that affects a pressure change

τp is the time constant for the coupling

p0 is the target pressure
An extra term is added to the equations of motion:

Velocity term Extra term

While the volume changes accordingly:

The pressure change is related to the isothermal compressibility, κT

p
κT
κT V κT

κT

κT One can easily see, that only that

ratio κT/τp enters in the equations of
motion.
 κT

κT
- τp
κT
 Andersen barostat

Equations of motion
 Parrinello-Rahman Barostat
• For the simulation of crystals, scaling of volume is not sufficient
• Parrinello-Rahman takes care of change in shape as volume of the system

CHOLESTEROL
Fitting the AA/CG model
with Cholesterol Crystal
structure will ensure the
correct phase segregation
in bilayer

COARSE-GRAINED
ALL-ATOM

CHOL-CRYSTAL(AA) CHOL-CRYSTAL(CG)
50
SHIEH, HOARD AND NORDMAN, Acta Cryst. B37, 1538, 1981
Nose-Hoover thermo- and baro-stats
 Equilibration and Production Runs

Equilibration run Production run

• Trajectory in the production run should be used for computation

of equilibrium averages of the system properties
 System Static of Equilibrium Properties

• Thermodynamic Properties

• Kinetic Energy:
1 N
K . E. =  mi vi2
2 i

• Temperature: 2
T= K . E.
3 Nk B
 System Static of Equilibrium Properties

N
• Configuration Energy: Uc =   V (rij )
i j i

1  
N −1 N
• Pressure: PV = Nk T −
B
3
 rij  fij
i =1 j i

3 2 2 3 Nk B
• Specific Heat:  (Uc ) 2
NVE
= Nk B T (1 − )
2 2Cv
 System Properties: Static (3)

• Microscopic Structural Properties

• Pair correlation (Radial Distribution Function):
N
n( r ) V
g( r ) = = 2
4  r r N
2    (r − rij )
i j i

• Structure factor:

S (k ) = 1 + 4  
sin(kr )
(g (r ) − 1) r 2 dr
0 kr
Note: S(k) available from x-ray/neutron scattering experiment
Radial Distribution Function (RDF) or g(r)
4
Typical RDF
First Second Third
Solvation Solvation Solvation
Shell Shell Shell

g(r)

1.0

separation (r)
 X-RAY SCATTERING STRUCTURE
In general, structure of a condensed phase system is determined by
☼ X-ray scattering (scattering by electrons)
☼ Neutron Scattering (scattering by nuclei)
☼ NMR, Raman, IR etc
Our focus has been on X-ray scattering structure of ILs

I(θ) vs. 2θ
Ionic q= (4π/λ)sin(θ)
Liquid
I(q) vs. q
I (q) −  xi f i (q)
2

S (q) = i
2
n 
  xi f i ( q ) 
2θ is scattering angle  i =1 

q= (4π/λ)sin(θ) scattering wave number S(q) vs. q

J. P. Hansen and I. R. McDonald, Theory of Simple Liquids: Elsevier, New York, 2013 61
Structure Function from Experiment and Simulation
I (q) −  xi f i (q)
2

Experimental S (q) = i
2
Structure Function n 
 i i 
x f ( q )
 i =1 


sin qr
 o  xi x j f i (q) f j (q)  4r 2 ( g ij (r ) − 1) dr
Simulated qr
S (q) =
i j 0
2
Structure Function n 
 i i 
x f ( q )
 i =1 

• xi is fraction of atoms of type i gij(r)=nij(r)dr/njid(r)dr

• fi(q) is atomic form factor
• gij(r) is the radial distribution function for atom types i and j
• ρo is the total number density of the system
Computationally, decomposition of S(q) is easier as we know the
coordinates of the atoms 62
 Properties
• With help of GROMACS, we can calculate both structural and dynamical properties.
1. Structural Properties:

a. Radial Distribution Function, g(r):

𝑛 𝑟 𝑉
𝑔 𝑟 = = σ𝑖 σ𝑁
𝑗≠1 𝛿 𝑟 − 𝑟𝑖𝑗
4𝜋𝜌𝑟 2 ∆𝑟 𝑁2

gmx_mpi rdf -f traj_comp.xtc -n index.ndx -o rdf.xvg

b. Structure Function, S(q):

∞ sin 𝑞𝑟
𝑆 𝑞 = 1 + 4𝜋𝜌 ‫׬‬0 (𝑔 𝑟 − 1) 𝑟 2 𝑑𝑟
𝑞𝑟
gmx_mpi saxs -f traj_comp.xtc -s topol.tpr -n index.ndx -sq sq.xvg