Comparative Study of NAMD and GROMACS

Yanbin Wu, Joonho Lee and Yi WangTeam Project for Phy466

May 11, 2007

Outline

Motivation

Simulation Set-up

Procedure

Result and analysis

Conclusion

Motivation (1) NAMD and GROMACS

GROMACS:

developed in the Netherlands.Fast, free.

NAMD: developed in Urbana, IL.Parallel, fast for big systems, free.

Motivation (2) Compare two packages

Both are widely used MD packages. Different code implementation in the two

packages may cause different results Generally, one group mainly uses one package

Good chance to compare two packages !!!

Simulation Setup (1)

SimulationPackage

runningparameter

model(topological)

force field

Implementation

RESULTS

Simulation Setup (2) Algorithm

Running parameter Initial system

Size, composition Coordinate, velocity

Force field LJ parameter

Model Charge, bonding, angle parameter

Code implementation Black box

Procedure Find a zero point

NVE NVT

Compare different water models TIP3P SPCE

Compare different temperature control schemes Langevin Nose Hoover Berendsen

Simulation system The simplest system

Water Solvent of life Simple & isotropic Rich in experimental data

Water+Ions Ensembles

NVE NVT

Langevin, Nose-hoover, Berendsen

Water Model: SPCESPC/E rigid model (Berendsen et al., 1987)

q(h) = 0.4238, q(O) = - 0.8476 O-H distance = 1 (Å) H-O-H angle = 109.47 ° LJ parameter

A = 0.37122(kJ/mol)1/6.nm and B = 0.3428 (kJ/mol)1/12.nm

6 12

LJ

A BV

r r⎛ ⎞ ⎛ ⎞=− +⎜ ⎟ ⎜ ⎟⎝ ⎠ ⎝ ⎠

Water Model: TIP3PTIP3P flexible model (Mahoney and Jorgensen, 2000)

q(h) = 0.417, q(O) = - 0.834 O-H distance = 0.9572 (Å) H-O-H angle = 104.52 °

LJ parameter

= 0.1521, =3.15061(Å)

12 6

4 w wLJ wV

r r

σ σε⎡ ⎤⎛ ⎞ ⎛ ⎞= −⎢ ⎥⎜ ⎟ ⎜ ⎟⎝ ⎠ ⎝ ⎠⎢ ⎥⎣ ⎦

ε σ

Temperature control schemes Langevin

Introduce a random force and friction coefficient

Nose-hoover Introduce a thermal reservoir and a friction term in the eq. of motion

Berendsen Weak coupling first-order kinetics to an external heath bath with a given

temperature

0T TdT

dt τ−

=

2

2i i i

i

d d

dt m dtξ= −

r F r0

1( )

dT T

dt Q

ξ= −

d 2ri

dt2=

Fi

mi

−ξdri

dt+ r

o

< ri

o

(t)r j

o

(t+ s) >=2miξikBTδ(s)δ ij

Results and Analysis (1) Zero point

NVE1) 0.25 ns NVT to bring temperature up to 300K.2) 1 ns NVE.

Important: start with the same velocity and coordinate in both packages.

NVT1 ns NVT using Langevin dynamics temperature control, damping coefficient 5/ps.

NVE Zero Point

GROMACS NAMD

Water model Tip3p Tip3p

Diffusion coefficient (10-5cm2/s) 4.9799 (+/- 0.0012) 5.278 (+/-0.012)

5.6%difference

NVT Zero Point

GROMACS NAMD

Water model Tip3p Tip3p

Temperature control scheme Langevin (5) Langevin (5)

Diffusion coefficient (10-5 cm2/s) 2.5676 (+/-0.00009) 2.769 (+/-0.002)

7.3%difference

Results and Analysis (2) Different water models

1 ns NVT using Langevin dynamics with = 5/ps. Two different water models: SPCE and TIP3P. Most commonly used water models.

*SPCE and TIP3P water models exhibit similar dynamic properties in GROMACS.

SPCE TIP3P

5 2.5758 (+/- 0.00013) 2.5676 (+/-0.00009)

0.032% difference

Results and Analysis (3) Damping in Langevin Dynamics

1 ns NVT via Langevin dynamics with = 1, 5, 10 /ps.

*Damping affects the diffusion of water dramatically.*=5/ps best reproduces the experimental result.

GROMACS (TIP3P) NAMD (TIP3P)

1 3.7263 (+/-0.00063) 4.259 (+/-0.025)

5 2.5676 (+/-0.00009) 2.769 (+/-0.002)

10 1.8515 (+/- 0.00012) 1.958 (+/-0.003)

Results and Analysis (4) Different temperature control schemes

1 ns NVT using Langevin dynamics with = 5/ps 1 ns NVT using Nose-hoover thermostat with τ=0.1 ps 1 ns NVT using Berendsen thermostat with τ=0.1 ps

*Different temperature control schemes can achieve similar results with well-chosen parameters.

GROMACS(SPCE) Diffusion coefficient (10-5 cm2/s)

Langevin 2.5676 (+/- 0.00009)

Berendsen 2.6539 (+/- 0.00035)

Nose-Hoover 2.5584 (+/- 0.00016)

Results and Analysis (5) Water in the water+ion system

PackageTemperature control scheme

water model /force field Diffusion coefficient (10-5 (cm2/s))

NAMD Langevin (5)tip3p (namd) /CHARMM 2.2247 (+/- 0.0015)

GROMACS

Berendsenspce(gromacs)/GROMACS 2.3026 (+/- 0.00027)

Berendsenspce(reference)/ reference 2.4140 (+/- 0.00006)

Nose-hooverspce(gromacs)/GROMACS 2.3235 (+/- 0.00024)

Nose-hooverspce(reference)/ reference 2.4362 (+/- 0.00036)

Na+ in the water+ion system

Results and Analysis (5)

PackageTemperature control scheme

water model /force field Diffusion coefficient (10-5 (cm2/s))

NAMD Langevin (5)tip3p (namd) /CHARMM 0.8200 (+/- 0.0250)

GROMACS

Berendsenspce(gromacs)/GROMACS 0.9194 (+/- 0.00120)

Berendsenspce(reference)/ reference 1.3675 (+/- 0.00069)

Nose-hooverspce(gromacs)/GROMACS 1.0353 (+/- 0.00021)

Nose-hooverspce(reference)/ reference 1.2700 (+/- 0.00033)

Cl- in the water+ion system

Results and Analysis (5)

PackageTemperature control scheme

water model /force field Diffusion coefficient (10-5 (cm2/s))

NAMD Langevin (5)tip3p (namd) /CHARMM 1.1125 (+/- 0.0130)

GROMACS

Berendsenspce(gromacs)/GROMACS 1.3300 (+/- 0.00064)

Berendsenspce(reference)/ reference 1.6091 (+/- 0.00100)

Nose-hooverspce(gromacs)/GROMACS 1.3517 (+/- 0.00050)

Nose-hooverspce(reference)/ reference 1.4956 (+/- 0.00061)

Results and Analysis (5) Radial distribution of oxygen - oxygen

0 0.5 1 1.50

0.5

1

1.5

2

2.5

3

r(nm)

g(r)

oxygen-oxygen

Beren-gromacs

Beren-reference

Nose -gromacsNose -reference

NAMD

0.2 0.25 0.3 0.35 0.4

2.4

2.5

2.6

2.7

2.8

2.9

Radial distribution of oxygen – Cl-

Results and Analysis (5)

0 0.5 1 1.50

0.5

1

1.5

2

2.5

3

3.5

4

4.5

r(nm)

g(r)

oxygen - Cl-

Beren-gromacs

Beren-reference

Nose -gromacsNose -reference

NAMD

0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55

3

3.2

3.4

3.6

3.8

4

4.2

Radial distribution of oxygen – Na+

Results and Analysis (5)

0 0.5 1 1.50

1

2

3

4

5

6

7

8

9

r(nm)

g(r)

oxygen - Na+

Beren-gromacs

Beren-reference

Nose -gromacsNose -reference

NAMD

0.16 0.18 0.2 0.22 0.24 0.26 0.28 0.36.6

6.8

7

7.2

7.4

7.6

7.8

8

8.2

8.4

8.6

Conclusion The two packages GROMACS and NAMD produce similar

results (within tolerance) using the same set of parameters.

Damping coefficient affects the dynamics significantly and has to be chosen with caution.

Different temperature control schemes may generate similar dynamic properties.

Two different water models, SPCE and TIP3P were compared and only minor difference was observed regarding the diffusion of water.

Discussion

Energy conservation in NVE simulations Neighbor list update frequency Switch or shift function is required, instead of

cutoff PME

Damping coefficient in NVT simulations Balance temperature fluctuation and disturbance

to the motion of the system. Different temperature control schemes

Zero point (water+ion, NVT)GROMACS NAMD

Forcefield CHARMM CHARMM

watermodel(bonding) tip3p(namd) tip3p(namd)

Temperature control scheme Langevin (5) Langevin (5)

Diffusion coefficient 10-5 (cm2/s)

Water 1.6556 (+/-0.00020) 2.2247 (+/-0.0006)

Na+ 0.5409 (+/-0.00031) 0.8200 (+/-0.0250)

Cl- 0.9766 (+/-0.00034) 1.1125 (+/-0.0130)

Water Model (3)

Package water model

NAMD

TIP3P(NAMD)

O / H

2.4895e-3 2.4248e-6

3.1540e-9 1.2921e-17

GROMACS

TIP3P(GROMACS) 2.4889e-2 2.4352e-6

SPCE(GROMACS) 2.6171e-3 2.6331e-6

SPCE(reference) 2.6341e-3 2.6679e-6

6C 12C

6 126 12LJ

C CV

r r⎛ ⎞ ⎛ ⎞=− +⎜ ⎟⎜ ⎟

⎝ ⎠⎝ ⎠

NVE Zero PointGROMACS NAMD

Forcefield CHARMM CHARMM

watermodel(bonding) tip3p(namd) tip3p(namd)

Diffusion coefficient 10-5 (cm2/s) 2.4890 (+/-0.00096) 5.278 (+/-0.012)