Comparative Study of NAMD and GROMACS

1. Comparative Study of NAMD and GROMACS Yanbin Wu, Joonho Lee and Yi Wang Team Project for Phy466 May 11, 2007

2. Outline • Motivation • Simulation Set-up • Procedure • Result and analysis • Conclusion

3. Motivation (1) • NAMD and GROMACS GROMACS: developed in the Netherlands. Fast, free. NAMD: developed in Urbana, IL. Parallel, fast for big systems, free.

4. 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 !!!

5. Simulation Setup (1) running parameter Implementation Simulation Package RESULTS model (topological) force field

6. 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

7. Procedure • Find a zero point • NVE • NVT • Compare different water models • TIP3P • SPCE • Compare different temperature control schemes • Langevin • Nose Hoover • Berendsen

8. Simulation system • The simplest system • Water • Solvent of life • Simple & isotropic • Rich in experimental data • Water+Ions • Ensembles • NVE • NVT • Langevin, Nose-hoover, Berendsen

9. Water Model: SPCE SPC/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

10. Water Model: TIP3P TIP3P 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)

11. 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

12. Results and Analysis (1) • Zero point • NVE • 0.25 ns NVT to bring temperature up to 300K. • 1 ns NVE. Important: start with the same velocity and coordinate in both packages. • NVT 1 ns NVT using Langevin dynamics temperature control, damping coefficient 5/ps.

13. NVE Zero Point 5.6% difference

14. NVT Zero Point 7.3% difference

15. 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. 0.032% difference

16. 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.

17. 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 =0.1 ps • 1 ns NVT using Berendsen thermostat with =0.1 ps *Different temperature control schemes can achieve similar results with well-chosen parameters.

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

19. Results and Analysis (5) • Na+ in the water+ion system

20. Results and Analysis (5) • Cl- in the water+ion system

21. Results and Analysis (5) • Radial distribution of oxygen - oxygen

22. Results and Analysis (5) • Radial distribution of oxygen – Cl-

23. Results and Analysis (5) • Radial distribution of oxygen – Na+

24. 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.

25. 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

26. Zero point (water+ion, NVT)

27. Water Model (3)

28. NVE Zero Point